version date: 1 December 2006 EXERC|sEⅢ2 A LABORATORY COURSE IN MEDICINAL CHEMISTRY INTRODUCING MOLECULAR MODELING Ivone Carvalho*, Monica T Pupo, Aurea D. L. Borges, and Lilian SCBernardes Departmento de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de s Paulo, Av. do cafe s/n 14040-903. Ribeirao preto sP. Brazil E-mail: carronal@usp. br Abstract: A laboratory course in medicinal chemistry introducing molecular modeling. Molecular modeling is an important and useful tool in drug design and for predicting biological activity in library compounds. A wide variety of computer programs and methods have been developed to visualize the 3D geometry and to calculate the physicochemical properties of drugs. In this paper, we describe a practical approach to molecular modeling as a powerful tool to study structure-activity relationship in drugs such as antibacterials, hormones, and cholinergic and adrenergic agents. Early in the course, the students learn how to draw 3d structures and to use them to perform conformational and molecular analyses. Thus, they may compare drugs with similar pharmacological activities by superimposing their structures and evaluating geometry and physical properties Keywords: molecular modeling; conformational analysis; structure-activity relationships INTRODUCTION Planning and selecting educational activities in the teaching of medicinal chemistry are ever constant and necessary tasks in adapting program contents to meet the challenges of a world in permanent change. Transformations should direct the course in medicinal chemistry to favor the use of new technological resources and contribute to develop both alternative ways and the students critical thinking. Some methodological strategies should be incorporated into the teaching of medicinal chemistry, thus promoting the teaching- learning processes The classical structure-activity relationship(SAR) studies implied the synthesis of several, structurally related analogs to a lead compound and successive biological activity tests. After decades of SAR research, some general rules on the influence of specific structural changes on biological activity could be drawn, including the size and shape of the carbon chain, the nature and rate of substitution, and stereochemistry of lead compounds SAR and the traditional techniques of molecular modifications are still important tools in <www.iupac.org/publications/cd/medicinalchemistry/>
1 EXERCISE III.2 A LABORATORY COURSE IN MEDICINAL CHEMISTRY INTRODUCING MOLECULAR MODELING Ivone Carvalho*, Mônica T. Pupo, Áurea D. L. Borges, and Lilian S. C. Bernardes Departmento de Ciências Farmacêuticas de Ribeirão Preto, Universidade de S. Paulo, Av. do café s/n 14040-903, Ribeirão Preto, SP, Brazil E-mail: carronal@usp.br Abstract: A laboratory course in medicinal chemistry introducing molecular modeling. Molecular modeling is an important and useful tool in drug design and for predicting biological activity in library compounds. A wide variety of computer programs and methods have been developed to visualize the 3D geometry and to calculate the physicochemical properties of drugs. In this paper, we describe a practical approach to molecular modeling as a powerful tool to study structure–activity relationship in drugs such as antibacterials, hormones, and cholinergic and adrenergic agents. Early in the course, the students learn how to draw 3D structures and to use them to perform conformational and molecular analyses. Thus, they may compare drugs with similar pharmacological activities by superimposing their structures and evaluating geometry and physical properties. Keywords: molecular modeling; conformational analysis; structure–activity relationships. INTRODUCTION Planning and selecting educational activities in the teaching of medicinal chemistry are ever constant and necessary tasks in adapting program contents to meet the challenges of a world in permanent change. Transformations should direct the course in medicinal chemistry to favor the use of new technological resources and contribute to develop both alternative ways and the student’s critical thinking. Some methodological strategies should be incorporated into the teaching of medicinal chemistry, thus promoting the teachinglearning processes.1 The classical structure–activity relationship (SAR) studies implied the synthesis of several, structurally related analogs to a lead compound and successive biological activity tests. After decades of SAR research, some general rules on the influence of specific structural changes on biological activity could be drawn, including the size and shape of the carbon chain, the nature and rate of substitution, and stereochemistry of lead compounds. SAR and the traditional techniques of molecular modifications are still important tools in <www.iupac.org/publications/cd/medicinal_chemistry/> version date: 1 December 2006
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
version date: 1 December 2006 EXPERIMENTAL Drawing, conformational, and molecular analysis of drugs Drawing and 3D visualization Several easily utilized programs are available for building bidimensional molecules like Chem Window, Isis Draw, and Chem Draw. Accurate and high-quality figures and diagrams can be elaborated with the help of such programs that frequently contribute to documentation and communication in science The students learn the resources available in the main menu of chem draw and Chem3D and how to utilize the tool and template selection to design chemical structures The stereochemical aspects are discussed in depth and through exercises, they are able to correctly represent the asymmetrical carbons of drugs like benzylpenicillin(1)and estramustine(2), Fig. 1. Eventually, the structures can be drawn in perspective representing the molecules in the projections of Fisher, Newman, and Haworth 量昔 Benzylpenicillin Estramustine (1) C16HI8N2O4s Molecular weight. 334.39 C23H30CINNa2O6P C.5747:H.5.43:N.8.38 Molecular weight: 564.35 C.4895:H536:Cl.12.56:N,248 O.19.14:S.959 Na.8.15:O.17.01:P.549 Fig 1 Drug drawings showing relevant stereochemical features( ChemDraw) Several molecular properties can be calculated and/or represented in some of the programs as well as the molecular formulae, molecular weights and the theoretical elementary analysis. More sophisticated programs like ChemDraw UItra can, in addition predict H and C chemical shifts in NMR of chemical compounds, their freezing and melting points, log P, molar refractivity, and heat of formation, besides furnishing the correct chemical name (IUPAC) The students are trained to chemically recognize heterocyclic rings, frequently present in drugs, through the use of the main menu of Chem Draw by clicking on"Edit and Insert name as Structure". By introducing the English ring name in the dialog box, it is possible to visualize the corresponding chemical structure in the drawing window and the accepted IUPAC nomenclature, which helps the student build complex molecules In the Chem3D program, drugs are three-dimensionally visualized, by the grad building of bonds based on information on their length and position angles. More complex molecules can be obtained by alternating several of the available resources such as drawing <www.iupac.org/publications/cd/medicinalchemistry/>
3 EXPERIMENTAL Drawing, conformational, and molecular analysis of drugs Drawing and 3D visualization Several easily utilized programs are available for building bidimensional molecules like ChemWindow, Isis Draw, and ChemDraw. Accurate and high-quality figures and diagrams can be elaborated with the help of such programs that frequently contribute to documentation and communication in science. The students learn the resources available in the main menu of ChemDraw6 and Chem3D7 and how to utilize the tool and template selection to design chemical structures. The stereochemical aspects are discussed in depth and through exercises, they are able to correctly represent the asymmetrical carbons of drugs like benzylpenicillin (1) and estramustine (2), Fig. 1. Eventually, the structures can be drawn in perspective, representing the molecules in the projections of Fisher, Newman, and Haworth. O O H N N S H H COOH N O CH3 OPO3Na2 O Cl Cl H H Benzylpenicillin (1) Estramustine phosphate (2) C16H18N2O4S Molecular weight.: 334.39 C, 57.47; H, 5.43; N, 8.38; O, 19.14; S, 9.59 C23H30Cl2NNa2O6P Molecular weight: 564.35 C, 48.95; H, 5.36; Cl, 12.56; N, 2.48; Na, 8.15; O, 17.01; P, 5.49 H Fig. 1 Drug drawings showing relevant stereochemical features (ChemDraw). Several molecular properties can be calculated and/or represented in some of the programs as well as the molecular formulae, molecular weights and the theoretical elementary analysis. More sophisticated programs like ChemDraw Ultra8 can, in addition, predict 1 H and 13C chemical shifts in NMR of chemical compounds, their freezing and melting points, log P, molar refractivity, and heat of formation, besides furnishing the correct chemical name (IUPAC). The students are trained to chemically recognize heterocyclic rings, frequently present in drugs, through the use of the main menu of ChemDraw by clicking on “Edit” and “Insert name as Structure”. By introducing the English ring name in the dialog box, it is possible to visualize the corresponding chemical structure in the drawing window and the accepted IUPAC nomenclature, which helps the student build complex molecules. In the Chem3D7 program, drugs are three-dimensionally visualized, by the gradual building of bonds based on information on their length and position angles. More complex molecules can be obtained by alternating several of the available resources such as drawing <www.iupac.org/publications/cd/medicinal_chemistry/> version date: 1 December 2006
version date: 1 December 2006 tools, whole substructures ready in the program and the dialog box, where formulae in linear representation are typed. In parallel, molecules generated in ChemDraw(copy)can be converted to the 3D model in Chem3D (paste), as shown in Fig. 2 for sulfamethoxazole(3) CH3 H2N (3) Fig. 2 Conversion of the 3D sulfamethoxazole (3)structure into the cylindrical bond 3D display( ChemDraw- Chem In the Chem3D program, the molecule can be drawn in different formats, such backbone, ball and stick, and space filling by using standard length and bond angle values, Fig 3 3c) Fig 3 Different representations of sulfamethoxazole: (3a)wire,(3b)cylinder and sphere, (3c)cylinder, and (3d) space filling( Chem3D) Handling 3D molecular models from Chem3D or Molecular Modeling Pro programs can assess relevant stereofeatures of drugs, allowing information about the size volume, and shape of the molecules The importance of the stereochemistry in the mechanism of action of drugs is illustrated by epinephrine (4)and propranolol (5), acting on B-adrenergic receptors, Fig. 4 Compounds 4 and 5 can be easily drawn in their active configurations, R and s, respectively, by rotating the molecules around the x,Y, z axis and attributing according to the classical rule of Cahn-Ingold-Prelog. The configurations of the asymmetrical carbon in the side chains are apparently opposite, due to r and s nomenclature, but in comparison the 3D representations show that the disposition and spatial orientation of the hydroxyl groups are similar, both directed to the same face. The difference in their naming, R and s, is due to the priority rule, the aryloxy group in the antagonist(5) has priority over the methylenamino group of the side chain, which is not the case in the epinephrine molecule <www.iupac.org/publications/cd/medicinalchemistry/>
4 tools, whole substructures ready in the program and the dialog box, where formulae in linear representation are typed. In parallel, molecules generated in ChemDraw (“copy”) can be converted to the 3D model in Chem3D (“paste”), as shown in Fig. 2 for sulfamethoxazole (3). H2N N H S N O O O CH3 (3) Fig. 2 Conversion of the 3D sulfamethoxazole (3) structure into the cylindrical bond 3D display (ChemDrawChem3D). In the Chem3D program, the molecule can be drawn in different formats, such as backbone, ball and stick, and space filling by using standard length and bond angle values, Fig. 3. (3a) (3b) ( (3c) 3d) Fig. 3 Different representations of sulfamethoxazole: (3a) wire, (3b) cylinder and sphere, (3c) cylinder, and (3d) space filling (Chem3D). Handling 3D molecular models from Chem3D7 or Molecular Modeling Pro9 programs can assess relevant stereofeatures of drugs, allowing information about the size, volume, and shape of the molecules. The importance of the stereochemistry in the mechanism of action of drugs is illustrated by epinephrine (4) and propranolol (5), acting on β-adrenergic receptors, Fig. 4. Compounds 4 and 5 can be easily drawn in their active configurations, R and S, respectively, by rotating the molecules around the X, Y, Z axis and attributing according to the classical rule of Cahn–Ingold–Prelog. The configurations of the asymmetrical carbon in the side chains are apparently opposite, due to R and S nomenclature, but in comparison, the 3D representations show that the disposition and spatial orientation of the hydroxyl groups are similar, both directed to the same face. The difference in their naming, R and S, is due to the priority rule, the aryloxy group in the antagonist (5) has priority over the methylenamino group of the side chain, which is not the case in the epinephrine molecule (4).10 <www.iupac.org/publications/cd/medicinal_chemistry/> version date: 1 December 2006
version date: 1 December 2006 3D conversion active isomer r 3D conversion Propranolol(5) active isomer s Fig 4 Conformations of R-epinephrine(4)and S-propranolol (5)with distinct configuration descriptors Cahn-Ingold-Prelog priority rules), but with the stereogenic center in the same spatial disposition The importance of the shape and size of the molecule is illustrated by trans diethylstilbestrol (6)used to mimic estradiol, the natural hormone(7), Fig. 5. Comparing the interatomic distances in the natural and synthetic products, it can be seen that only the trans-isomer(6)has the desired distances between carbons containing hydroxyl groups around 9.0 A. The corresponding cis-isomer(8)shows distances of 5.9 A, quite different from the estradiol molecule(8.6A) <www.iupac.org/publications/cd/medicinalchemistry/>
5 O N H OH 3D conversion Propranolol (5) active isomer S HO HO H N CH3 OH 3D conversion Epinephrine (4) active isomer R Fig. 4 Conformations of R-epinephrine (4) and S-propranolol (5) with distinct configuration descriptors (Cahn–Ingold–Prelog priority rules), but with the stereogenic center in the same spatial disposition. The importance of the shape and size of the molecule is illustrated by transdiethylstilbestrol (6) used to mimic estradiol, the natural hormone (7), Fig. 5. Comparing the interatomic distances in the natural and synthetic products, it can be seen that only the trans-isomer (6) has the desired distances between carbons containing hydroxyl groups, around 9.0 Å. The corresponding cis-isomer (8) shows distances of 5.9 Å, quite different from the estradiol molecule (8.6 Å).11 <www.iupac.org/publications/cd/medicinal_chemistry/> version date: 1 December 2006