title: Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions.
abstract: Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners' (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions.
authors.affiliation: Laboratory of Computational and Structural Physical-Chemistry for Nanosciences and QSAR, Department of Biology-Chemistry, West University of Timi&#351;oara, Pestalozzi Str. 16, RO-300115 Timisoara, Romania. mv_putz@yahoo.com.|Laboratory of Renewable Energies-Photovoltaics, R &amp; D National Institute for Electrochemistry and Condensed Matter, Dr. A. Paunescu Podeanu Str. No. 144, RO-300569 Timisoara, Romania. mv_putz@yahoo.com.
authors.forename: Mihai V
authors.initials: MV
authors.lastname: Putz
authors.affiliation: Laboratory of Computational and Structural Physical-Chemistry for Nanosciences and QSAR, Department of Biology-Chemistry, West University of Timi&#351;oara, Pestalozzi Str. 16, RO-300115 Timisoara, Romania. cori_mam@yahoo.com.
authors.forename: Corina
authors.initials: C
authors.lastname: Duda-Seiman
authors.affiliation: Department of Medical Ambulatory, and Medical Emergencies, University of Medicine and Pharmacy "Victor Babes", Avenue C. D. Loga No. 49, RO-300020 Timisoara, Romania. duda.seiman@cardiologie.ro.
authors.forename: Daniel
authors.initials: D
authors.lastname: Duda-Seiman
authors.affiliation: Laboratory of Computational and Structural Physical-Chemistry for Nanosciences and QSAR, Department of Biology-Chemistry, West University of Timi&#351;oara, Pestalozzi Str. 16, RO-300115 Timisoara, Romania. putzanamaria@yahoo.com.|Institute of Chemistry Timișoara of the Romanian Academy, 24 Mihai Viteazul Bld., RO-300223 Timisoara, Romania. putzanamaria@yahoo.com.
authors.forename: Ana-Maria
authors.initials: AM
authors.lastname: Putz
authors.affiliation: Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Str. 91-95th Independentei, RO-050095 Bucharest, Romania. iuliaaim@yahoo.com.
authors.forename: Iulia
authors.initials: I
authors.lastname: Alexandrescu
authors.affiliation: Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Str. 91-95th Independentei, RO-050095 Bucharest, Romania. maria.mernea@bio.unibuc.ro.
authors.forename: Maria
authors.initials: M
authors.lastname: Mernea
authors.affiliation: Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Str. 91-95th Independentei, RO-050095 Bucharest, Romania. speranta.avram@gmail.com.
authors.forename: Speranta
authors.initials: S
authors.lastname: Avram
mesh_terms: D000465:Algorithms; D015195:Drug Design; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D021281:Quantitative Structure-Activity Relationship; D055672:Static Electricity
chemical_list: D008024:Ligands
keywords: chemical stericity; cross-validation; drug design; hydrophobicity; ligand binding; molecular mechanism; multi-linear correlation; quantitative structure-activity relationship (QSAR); statistical correlation; van der Waals interaction