version date: 1 December 2006 the search for new drugs, but they are expensive highly time-consuming, and eventually successful Chemical computer programs and the Web databases are important tools in the current search for and design of drugs. A series of interesting molecules can be rapidly screened as to their biological activity versus physicochemical properties. New therapeutic agents can be developed, analyzing theoretical data on structure-activity in the 3D form obtained through recent molecular modeling techniques. In a broad definition of medicinal chemistry, relating the invention, discovery, planning, identification, and preparation of biologically active compounds, to the study of its metabolism, mechanism of molecular action, and construction of SARs, it is highly important to insert and approach topics in molecular modeling in graduation courses on medicinal chemistry According to IUPAC, molecular modeling is an investigation of structures and molecular properties by using techniques of computational chemistry and graphic visualization aiming to obtain, under certain circumstances, a 3D representation Computer-assisted drug design( CADD)is described in many sites on the Internet, helping through tutorials, the investigation of receptor-ligant chemical interactions and the exploring of structural factors connected to biological effects. As a result, the integration of essential knowledge in organic chemistry, biochemistry, molecular biology, and pharmacology, contributes to the understanding of the mechanisms in drug molecular actions The laboratory course in medicinal chemistry is presented to the fifth-period Pharmacy students(30 h, 2 groups)in parallel to the theoretical course(60 h). After careful analysis of the different approaches, laboratory practices were directed to the study of geometry and properties of drugs, enabling the students to explore the chemical and molecular basis of the drug-receptor interaction, by employing computational techniques More specifically, the objectives are (i) conformational analysis of drugs by visualizing its 3D format (ii) analysis of the size and shape of the pharmacophore (ii) importance of the nature and rate of functional groups substitution (iv) stereochemical aspects of drugs and their relation to biological activity (v) to relate a single series of drugs trough structures and physical properties (vi) to predict molecular mechanisms involved in drug action Methods and computational resources employed in the drawing, accurate structural representation, and 3D visualization of drugs are initially presented in this paper; this is followed by showing the use of molecular modeling in the theoretical determination of physicochemical properties and comparison of data obtained with adrenergic and cholinergic drugs, active in the autonomic nervous system This approach significantly contributes both to an integration of theoretical and laboratory data in structure-activity of drugs, and to the implementation of practical courses in medicinal chemistry <www.iupac.org/publications/cd/medicinalchemistry/>2 the search for new drugs, but they are expensive, highly time-consuming, and eventually successful.2 Chemical computer programs and the Web databases are important tools in the current search for and design of drugs. A series of interesting molecules can be rapidly screened as to their biological activity versus physicochemical properties. New therapeutic agents can be developed, analyzing theoretical data on structure–activity in the 3D form, obtained through recent molecular modeling techniques. In a broad definition of medicinal chemistry, relating the invention, discovery, planning, identification, and preparation of biologically active compounds, to the study of its metabolism, mechanism of molecular action, and construction of SARs, it is highly important to insert and approach topics in molecular modeling in graduation courses on medicinal chemistry.3 According to IUPAC, molecular modeling is an investigation of structures and molecular properties by using techniques of computational chemistry and graphic visualization aiming to obtain, under certain circumstances, a 3D representation.4 Computer-assisted drug design (CADD) is described in many sites on the Internet, helping, through tutorials, the investigation of receptor-ligant chemical interactions and the exploring of structural factors connected to biological effects.5 As a result, the integration of essential knowledge in organic chemistry, biochemistry, molecular biology, and pharmacology, contributes to the understanding of the mechanisms in drug molecular actions. The laboratory course in medicinal chemistry is presented to the fifth-period Pharmacy students (30 h, 2 groups) in parallel to the theoretical course (60 h). After careful analysis of the different approaches, laboratory practices were directed to the study of the geometry and properties of drugs, enabling the students to explore the chemical and molecular basis of the drug–receptor interaction, by employing computational techniques. More specifically, the objectives are: (i) conformational analysis of drugs by visualizing its 3D format. (ii) analysis of the size and shape of the pharmacophore (iii) importance of the nature and rate of functional groups substitution (iv) stereochemical aspects of drugs and their relation to biological activity (v) to relate a single series of drugs trough structures and physical properties (vi) to predict molecular mechanisms involved in drug action Methods and computational resources employed in the drawing, accurate structural representation, and 3D visualization of drugs are initially presented in this paper; this is followed by showing the use of molecular modeling in the theoretical determination of physicochemical properties and comparison of data obtained with adrenergic and cholinergic drugs, active in the autonomic nervous system. This approach significantly contributes both to an integration of theoretical and laboratory data in structure–activity of drugs, and to the implementation of practical courses in medicinal chemistry. <www.iupac.org/publications/cd/medicinal_chemistry/> version date: 1 December 2006