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Latest advances in molecular topology applications for drug discovery

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Bibliography

  • Hansch C, Fujita T. p-sigma-pi analysis. A method for the correlation of biological activity and chemical structure. J Am Chem Soc 1964;86(8):1616-26
  • Cramer RD, Patterson DE, Bunce JD. Comparative molecular field analysis (CoMFA). 1. effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 1988;110(18):5959-67
  • Myint KZ, Xie X. Recent advances in fragment-based QSAR and multi-dimensional QSAR methods. Int J Mol Sci 2010;11(10):3846-66
  • Sippl W. 3D-QSAR using the GRID/GOLPE approach. Mol Interact Fields 2006;27:145-70
  • Lepšík M, Řezáč J, Kolář M, et al. The semiempirical quantum mechanical scoring function for in silico drug design. ChemPlusChem 2013;78(9):921-31
  • Rathore R, Sumakanth M, Reddy MS, et al. Advances in binding free energies calculations: QM/MM-based free energy perturbation method for drug design. Curr Pharm Des 2013;19(26):4674-86
  • Kerrigan JE. Molecular dynamics simulations in drug design. In: Sandhya Kortagere, editor. Silico models for drug discovery. Humana Press, New York, USA; 2013. p 95-113
  • Zhao H, Caflisch A. Molecular dynamics in drug design. Eur J Med Chem 2015;91:4-14
  • Caporuscio F, Tafi A. Pharmacophore modelling: A forty year old approach and its modern synergies. Curr Med Chem 2011;18(17):2543-53
  • Fang Y. Ligand-receptor interaction platforms and their applications for drug discovery. Expert Opin Drug Dis 2012;7(10):969-88
  • Basak SC, Mills D, Natarajan R, Gute BD. Predicting chemical reactivity and bioactivity of molecules from structure. Section title General physical chemistry; 2009. p 479-502
  • Natarajan R, Basak SC, Mills D, et al. Quantitative structure-activity relationship modeling of mosquito repellents using calculated descriptors. Croat Chem Acta 2008;81(2):333-40
  • Ivanciuc O. Topological indices. Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes. 2003. p 981-1003
  • Gálvez J, Gálvez-Llompart M, García-Domenech R. Application of molecular topology for the prediction of the reaction times and yields under solvent-free conditions. Green Chem 2010;12(6):1056-61
  • Gálvez J, Parreño M, Pla J, et al. Application of molecular topology to the prediction of water quality indices of alkylphenol pollutants. 2011
  • Gálvez-Llompart M, Recio MC, García-Domenech R. Topological virtual screening: A way to find new compounds active in ulcerative colitis by inhibiting NF-κB. Mol Divers 2011;15(4):917-26
  • Mérida S, Fustero S, M Villar V, et al. Efficacy and activity prediction by molecular topology of new drugs against the tetranychus urticae plague. Comb Chem High Throughput Screen 2013;16(6):473-83
  • Garcia-Domenech R, Zanni R, Galvez-Llompart M, Galvez J. Predicting antiprotozoal activity of benzyl phenyl ether diamine derivatives through QSAR multi-target and molecular topology. Mol Divers 2015;19(2):357-66
  • Gálvez J, Gálvez-Llompart M, García-Domenech R. Molecular topology as a novel approach for drug discovery. Expert Opin Drug Discov 2012;7(2):133-53
  • García-Domenech R, Gálvez J, de Julián-Ortiz JV, Pogliani L. Some new trends in chemical graph theory. Chem Rev 2008;108(3):1127-69
  • Galvez J, Galvez-Llompart M, Zanni R, Garcia-Domenech R. Molecular topology–dissimilar similarities. Drug Discov Today: Technol 2013;10(4):e475-81
  • Galvez J, Galvez-Llompart M, Garcia-Domenech R. Introduction to molecular topology: Basic concepts and application to drug design. Curr Comput Aided Drug Des 2012;8(3):196-223
  • Basak S, Ray S, Raychaudhury C, et al. Molecular topology and pharmacological action-a qsar study of tetrazoles using topological information-content (ic). Ircs Med Sci Biochem 1982;10(2):145-6
  • Basak S. Binding of barbiturates to cytochrome P450: A QSAR study using log P and topological indices. Med Sci Res 1988;16(28):1-282
  • Trinajstić N, Klein DJ, Randić M. On some solved and unsolved problems of chemical graph theory. Int J Quantum Chem 1986;30(S20):699-742
  • Randić M, Basak SC. A new descriptor for structure-property and structure-activity correlations. J Chem Inf Comput Sci 2001;41(3):650-6
  • Kier L, Hall L. The electrotopological state: Structure modeling for QSAR and database analysis. Topological indices and related descriptors in QSAR and QSPR 1999;491
  • Hall LM, Hall LH, Kier LB. Modeling drug albumin binding affinity with e-state topological structure representation. J Chem Inf Comput Sci 2003;43(6):2120-8
  • Kier LB, Hall LH. The generation of molecular structures from a Graph-Based QSAR equation. Quantitative Structure-Activity Relationships 1993;12(4):383-8
  • Hall LH, Maynard EL, Kier LB. QSAR investigation of benzene toxicity to fathead minnow using molecular connectivity. Environ Toxicol Chem 1989;8(9):783-8
  • Contrera JF, MacLaughlin P, Hall LH, Kier LB. QSAR modeling of carcinogenic risk using discriminant analysis and topological molecular descriptors. Curr Drug Discov Technolog 2005;2(2):55-67
  • Hall L, Hall L. QSAR modeling based on structure-information for properties of interest in human health. SAR QSAR Environ Res 2005;16(1-2):13-41
  • Devillers J, Balaban A. Topological indices and related descriptors in QSAR and QSPR. Gordon and Breach; Amsterdam, 1999
  • Balaban AT. A personal view about topological indices for QSAR/QSPR. ChemInform 2001;32:30
  • Bonchev D. 8. overall connectivity and topological complexity: A new tool for qspr/qsar. Topological Indices and Related Descriptors in QSAR and QSPAR 2000;361
  • Barigye SJ, Marrero-Ponce Y, Pérez-Giménez F, Bonchev D. Trends in information theory-based chemical structure codification. Mol Divers 2014;18(3):673-86
  • Galvez J, Garcia-Domenech R, de Julián-Ortiz JV, Soler R. Topological approach to drug design. J Chem Inf Comput Sci 1995;35(2):272-84
  • Gálvez J, Gomez-Lechón M, García-Domenech R, Castell J. New cytostatic agents obtained by molecular topology. Bioorg Med Chem Lett 1996;6(19):2301-6
  • Caboni L, Galvez-Llompart M, Gálvez J, et al. Molecular topology applied to the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2 H-pyrrole-5-one as a non-ligand-binding-pocket antiandrogen. J Chem Inf Model 2014;54(10):2953-66
  • Rios-Santamarina I, Garcia-Domenech R, Gálvez J, et al. New bronchodilators selected by molecular topology. Bioorg Med Chem Lett 1998;8(5):477-82
  • García-March F, García-Domenech R, Galvez J, Antón-Fos G. Julián-Ortiz Jd, Giner-Pons R, et al. Pharmacological studies of 1-(p-Chlorophenyl) propanol and 2-(1-Hydroxy-3-butenyl) phenol: Two new Non-narcotic analgesics designed by molecular connectivity. J Pharm Pharmacol 1997;49(1):10-15
  • Galvez-Llompart M, Zanni R, García-Domenech R. Modeling natural anti-inflammatory compounds by molecular topology. Int J Mol Sci 2011;12(12):9481-503
  • Galvez-Llompart M, Del Carmen Recio Iglesias M, Gálvez J, García-Domenech R. Novel potential agents for ulcerative colitis by molecular topology: Suppression of IL-6 production in caco-2 and RAW 264.7 cell lines. Mol Divers 2013;17(3):573-93
  • Gálvez-Llompart M, Zanni R, Romualdi P, García-Domenech R. Selection of nutraceutical compounds as COX inhibitors by molecular topology. Med Chem Res 2013;22(7):3466-77
  • Garcia-Domenech R, Zanni R, Galvez-Llompart M, Vicente de Julian-Ortiz J. Modeling anti-allergic natural compounds by molecular topology. Comb Chem High Throughput Screen 2013;16(8):628-35
  • Galvez J, García Domenech R, Garcia March F, Moliner Llusar R. inventors; Spain, assignee. Derivados del 1-(2,4 dimetil) fenil etanona. Compuestos con aplicaciones farmacológicas por su actividad analgésica y antiinflamatoria. Patent Application Country: Spain. Application: Universitat de Valencia (Estudi General),Spain; Priority Application Country: P.9101134. Patent Application Date 1991
  • Galvez J, García Domenech R, Garcia March F, Moliner Llusar R. inventors; Spain, assignee. Derivados del 2-(1-propenil) fenol. Compuestos con aplicaciones farmacológicas por su actividad analgésica y antiinflamatoria. Patent Application Country: Spain. Application: Universitat de Valencia (Estudi General),Spain; Priority Application Country: P.9101134. Patent Application Date 1991
  • Galvez J, Llompart J, Pal K. inventors; Spain, assignee. N,N-dicyclohexyl-(1S)-isoborneol-10-sulfonamide (MT103) and related compounds for the treatment of cancer. Patent Application Country: Application: US; US; Priority Application Country: US patent. US20040266732. 2004. Patent Application Date: 20040430; Priority Application Date: 20020920
  • Llompart J, Galvez J, Pal K. inventors Medisyn Technologies I, USA, assignee. Treatment of cancer with MT477 derivatives. Patent Application Country: Application: US; US; Priority Application Country: US patent. US20060014770. 2006. Patent Application Date: 20050711; Priority Application Date: 20040709
  • Mazier D, Mahmoudi N, Farhati K, et al. inventors Universite Pierre et Marie CURIE-Paris VI, Fr., Universite Paris Diderot - Paris 7, Universitat de Valencia, Assistance Publique - Hopitaux de Paris, assignees. Monensin derivatives for preventing and treating plasmodium infections. Patent Application Country: Application: WO; WO; Priority Application Country: EP patent. WO2009074649. 2009 0618; Patent Application Date: 20081211; Priority Application Date: 20071211
  • Galvez J, Llompart J, Land D, Pasinetti G. inventors Mount Sinai School of Medicine of New York University, USA, Medisyn Technologies I, assignees. Compositions for treatment of alzheimer’s disease using Aβ-reducing and/or Aβ-anti-aggregation compounds. Patent Application Country: Application: WO; WO; Priority Application Country: US patent. WO2010114636. 2010. Patent Application Date: 20100405; Priority Application Date: 20090403
  • Garfield RE, Balaban AT, Seitz WA. inventors University of Texas System, USA, Texas A & M University System, Garfield RE, Balaban AT, Seitz WA, assignees. Emulsions of perfluoro compounds as solvents for nitric oxide (NO). Patent Application Country: Application: WO; WO; Priority Application Country: US patent. WO9738579. 1997. Patent Application Date: 19970416; Priority Application Date: 19960417
  • Kier LB. inventor Ohio State University, assignee. Mesoionic thiadiazole bacterticides. Patent Application Country: Application: US; US patent. US3337398. 1967. Patent Application Date: 19651112
  • Young DC. Computational drug design: A guide for computational and medicinal chemists. John Wiley & Sons; 2009
  • Aguiar-Pulido V, Gestal M, Cruz-Monteagudo M, et al. Evolutionary computation and QSAR research. Curr Comput Aided Drug Des 2013;9(2):206-25
  • Materi W, Wishart DS. Computational systems biology in drug discovery and development: Methods and applications. Drug Discov Today 2007;12(7):295-303
  • Prado-Prado FJ, González-Díaz H, Santana L, Uriarte E. Unified QSAR approach to antimicrobials. part 2: Predicting activity against more than 90 different species in order to halt antibacterial resistance. Bioorg Med Chem 2007;15(2):897-902
  • Zanni R, Galvez-Llompart M, Galvez J, Garcia-Domenech R. QSAR multi-target in drug discovery: A review. Curr Comput Aided Drug Des 2014;10(2):129-36
  • Speck-Planche A, Kleandrova VV, Luan F, DS Cordeiro MN. Computational modeling in nanomedicine: Prediction of multiple antibacterial profiles of nanoparticles using a quantitative structure-activity relationship perturbation model. Nanomedicine 2015;10(2):193-204
  • Casañola-Martin GM, Le-Thi-Thu H, Pérez-Giménez F, et al. Multi-output model with Box–Jenkins operators of linear indices to predict multi-target inhibitors of ubiquitin–proteasome pathway. Mol Divers 2015;19(2):347-56
  • Speck-Planche A, Cordeiro M. Enabling virtual screening of potent and safer antimicrobial agents against noma: Mtk-QSBER model for simultaneous prediction of antibacterial activities and ADMET properties. Mini Rev Med Chem 2015;15(3):194-202
  • Gonzalez-Diaz H, Arrasate S, Gómez-SanJuan A, et al. General theory for multiple input-output perturbations in complex molecular systems. 1. linear QSPR electronegativity models in physical, organic, and medicinal chemistry. Curr Top Med Chem 2013;13(14):1713-41
  • Box GE, Jenkins GM. Time series analysis: Forecasting and control. revised edition Holden-Day; 1976
  • Speck-Planche A, Kleandrova VV, Luan F, DS Cordeiro MN. Computational modeling in nanomedicine: Prediction of multiple antibacterial profiles of nanoparticles using a quantitative structure-activity relationship perturbation model. Nanomedicine 2015;10(2):193-204
  • Kleandrova VV, Luan F, Gonz’lez-Díaz H, et al. Computational tool for risk assessment of nanomaterials: Novel QSTR-perturbation model for simultaneous prediction of ecotoxicity and cytotoxicity of uncoated and coated nanoparticles under multiple experimental conditions. Environ Sci Technol 2014;48(24):14686-94
  • Allen GI, Liu Z. A local poisson graphical model for inferring networks from sequencing data. NanoBioscience, IEEE Transactions on 2013;12(3):189-98
  • Leifer M, Poulin D. Quantum graphical models and belief propagation. Annals Physics 2008;323(8):1899-946
  • Langfeld K. Computational methods in quantum field theory. arXiv preprint arXiv:0711.3004. 2007
  • Wu W, Yang X, Pang Y, et al. A multifocus image fusion method by using hidden markov model. Opt Commun 2013;287:63-72
  • Vergara-Galicia J, J Prado-Prado F, Gonzalez-Diaz H. Galvez-markov network transferability indices: Review of classic theory and new model for perturbations in metabolic reactions. Curr Drug Metab 2014;15(5):557-64
  • Riera-Fernandez P, R Munteanu C, Martin-Romalde R, et al. Markov-Randić indices for QSPR re-evaluation of metabolic, parasite-host, fasciolosis spreading, brain cortex and legal-social complex networks. Curr Bioinformat 2013;8(4):401-15
  • Cayley A. On the mathematical theory of isomers. Philos Mag 1874;67(5):444-6
  • A Tudoran M, V Putz M. Molecular graph theory: From adjacency information to colored topology by chemical reactivity. Curr Organic Chem 2015;19(4):359-86
  • Rouvray D. Topological Indies as Chemical Behavior Descriptors. 1985
  • Nandi S, C Bagchi M. Importance of kier-hall topological indices in the QSAR of anticancer drug design. Curr Comput Aided Drug Des 2012;8(2):159-70
  • Martínez-Santiago O, Millán-Cabrera R, Marrero-Ponce Y, et al. Discrete derivatives for Atom-Pairs as a novel Graph-Theoretical invariant for generating new molecular descriptors: Orthogonality, interpretation and QSARs/QSPRs on benchmark databases. Mol Informat 2014;33(5):343-68
  • Bonchev D. A simple integrated approach to network complexity and node centrality. Analysis of complex networks: from biology to linguistics. John Wiley & Sons; 2009. p 47-53
  • Mueller LA, Kugler KG, Graber A, et al. Structural measures for network biology using QuACN. BMC Bioinformat 2011;12:492
  • Furtula B, Lekishvili G, Gutman I. A graph theoretical approach to cis/trans isomerism. J Serbian Chemi Soc 2014;79(7):805-13
  • Basak SC, Restrepo G, Villaveces JL, et al. Advances in mathematical chemistry and applications. 2014
  • Braun J, Gugisch R, Kerber A, et al. MOLGEN-CID A canonizer for molecules and graphs accessible through the internet. J Chem Inf Comput Sci 2004;44(2):542-8
  • Ghosh A, Nandy A. Graphical representation and mathematical characterization of protein sequences and applications to viral proteins. Adv Protein Chem Struct Biol 2011;83:1-42
  • Emmert-Streib F, Dehmer M, Varmuza K, Bonchev D. Statistical modelling of molecular descriptors in QSAR/QSPR. John Wiley & Sons, Hoboken, NJ, USA; 2012
  • Mekenyan O, Bonchev D, Trinajstic N. A topological characterization of cyclic structures with acyclic branches. Commun Math Comput Chem (MATCH) 1981;11:145-68
  • Willett P. Similarity searching using 2D structural fingerprints. In: Jürgen Bajorath, editor. Chemoinformatics and Computational Chemical Biology. Humana Press, New York, USA; 2011. p. 133-58
  • Podolyan Y, Karypis G. Common pharmacophore identification using frequent clique detection algorithm. J Chem Inf Model 2008;49(1):13-21
  • Ghosh P, Vracko M, Chattopadhyay AK, Bagchi MC. On application of constitutional descriptors for merging of quinoxaline data sets using linear statistical methods. Chem Biol Drug Des 2008;72(2):155-62
  • Talevi A, Bruno-Blanch LE. Virtual screening: An efficient tool for the development of new drugs in latin america. Latin Am J Pharm 2009;28(1):141-50
  • Talevi A, Enrique AV, Bruno-Blanch LE. Anticonvulsant activity of artificial sweeteners: A structural link between sweet-taste receptor T1R3 and brain glutamate receptors. Bioorg Med Chem Lett 2012;22(12):4072-4
  • Galvez J, Galvez-Llompart M, Zanni R, Garcia-Domenech R. Advances in the molecular modeling and quantitative structure-activity relationship-based design for antihistamines. Expert Opin Drug Discov 2013;8(3):305-17
  • Garcia-Domenech R, Zanni R, Galvez-Llompart M, Vicente de Julián-Ortiz J. Modeling anti-allergic natural compounds by molecular topology. Combinatorial Chemistry & High Throughput Screening 2013;16(8):628-35
  • Wang J, Land D, Ono K, et al. Molecular topology as novel strategy for discovery of drugs with Aβ lowering and anti-aggregation dual activities for Alzheimer’s disease. PLoS One 2014;9(3):e92750
  • Zanni R, Galvez-Llompart M, Morell C, et al. Novel cancer chemotherapy hits by molecular topology: dual akt and Beta-catenin inhibitors. PLoS One 2015;10(4):e0124244
  • Garcia-Domenech R, Galvez-Llompart M, Zanni R, Galvez J. Modelling susceptibility to multi-target anaerobic bacteria by Molecular Topology. 8th International Symposium on Anaerobic Microbiology (ISAM8) Innsbruck; June 12-15; Austria; 2013
  • Vicente de Julian-Ortiz J, Zanni R, Galvez-Llompart M, Garcia-Domenech R. The prediction of human intestinal absorption based on the molecular structure. Curr Drug Metab 2014;15(4):380-8
  • Gálvez-Llompart M, Gálvez J, García-Domenech R, Kier LB. Modeling drug-induced anorexia by molecular topology. J Chem Inf Model 2012;52(5):1337-44
  • Gálvez-Llompart M, Gálvez J, García-Domenech R, Kier LB. Predicting dyspnea inducers by molecular topology. J Chem 2012;2013
  • Bellera CL, Balcazar DE, Vanrell MC, et al. Computer-guided drug repurposing: identification of trypanocidal activity of clofazimine, benidipine and saquinavir. Eur J Med Chem 2015;93:338-48

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