2023 Lecture 5 Stereochemistry + Biomolecules PDF

PHAR 7813 Principles of Drug Action I: Lecture 5 Understanding Drugs on the Molecular Level: Stereochemistry and Molecular Introduction to Biomolecules January 31st, 2023 Anthony W. G. Burgett, Ph.D. Department of Pharmaceutical Sciences...

PHAR 7813 Principles of Drug Action I: Lecture 5 Understanding Drugs on the Molecular Level: Stereochemistry and Molecular Introduction to Biomolecules January 31st, 2023 Anthony W. G. Burgett, Ph.D. Department of Pharmaceutical Sciences 1 Learning Objectives for This Lecture: Stereochemistry: 1) Define the terms concepts of stereochemistry, isomer, conformational isomer, substituents, and stereoisomers. 2) Describe what a conformational isomer is and why such isomers are often limited in drug molecules. 3) Identify which sp2 hybridized FGs can have multiple stereoisomers based on the substituents 4) Identify the requirements for a sp3 tetrahedron carbon to be stereocenter. 5) Define the concepts of chirality, asymmetry, stereochemical configuration, enantiomers, and diastereomers. 6) Identify how many possible stereochemical configurations are possible around any sp3 stereocenter, and recognize the names for the different possible stereochemical configurations around the sp3 stereocenter. 7) Explain why enantiomers of the same drug molecules have identical physical properties (i.e., solubility, melting point, etc.) but those enantiomers could have very different drug properties. 8) For a compound with two stereocenters, understand why that molecule will have two sets of enantiomers and that the one set of enantiomers are diastereomers to the other set of enantiomers. 9) Be able to define racemic mixture and be able to recognize the existence of the racemic mixture for a molecule based on the chemical structure (i.e., squiggly lines). 2 Learning Objectives for This Lecture: Biomolecules: 1) Be able to list and identify based on molecular structure the 4 major classes of biomolecules. 2) Provide a functional definition of the lipid class of biomolecules. 3) Describe how lipids organize to form lipid bilayers and identify the classes of lipid molecules involved in lipid bilayers. 4) Be able to identify steroids lipids, fatty acid lipids, triglycerides, and phospholipids based on their molecular structure. 5) Define and be able to recognize amino acid, peptide and protein. 6) Identify and be able to recognize the 4 parts of any amino acid 7) Identify all the FGs that bond together to polymerize amino acids into peptides/proteins 8) Explain why proteins can be defined as having stereochemistry. 9) Define and recognize carbohydrate molecules in open form, closed forms, and 3D drawing of the closed form, and the polymeric form (especially for glucose and ribose). 10) Identify how carbohydrates can exists as stereoisomers (i.e., diastereomers) 11) Define and recognize the terms saccharide, monosaccharide, disaccharide, and polysaccharide. 12) Identify the three components that make up nucleotides 13) Identify how nucleotides polymerize to make the nucleic acids DNA and RNA. 14) Recognize that nucleotides can have important biological activities other than be polymerized into DNA and RNA. 15) Be able to recognize ribose and deoxyribose in both closed and open forms, and be able to identify the 5 nucleobases that make up nucleotide 16) Be able to explain the differences on the molecule structural level between DNA and RNA. 3 Understanding Drugs on the Molecular Level The effects of stereochemistry on the drug molecule form/function: naproxen example. Dipole-dipole interaction between Naproxen has one sp3 stereocenter (shown in red) which is essential for oxygen ether FG and targeting binding and drug activity. protein Aromatic rings Compound with different bonding around this stereocenter (i.e., dispersion force stereocenter configuration) (shown below) are inactive compounds that interactions could NOT bind to the protein target. Hydrogen bonding between protein and carboxylate FG of naproxen The molecular form (i.e., shape and charges) dictates the molecular function…stereochemistry is important for molecular form. Organic Chemistry for Pharmacy: Review of stereochemistry Stereochemistry: study of the arrangement and properties of atoms in three-dimensional space. Isomers: different compound with the same molecular formula. (same atoms involved ) Constitutional Isomers vs. Stereoisomer (different bonds) vs. (different in 3D) Configurational vs. Conformational (non-rotational) vs. (bond rotation) Geometric (sp2) vs. Optical (sp3) (no stereocenters) vs. (stereocenters) Diastereomers vs. Enantiomers (not mirror images) vs. (mirror images) Organic Chemistry for Pharmacy: Review of stereochemistry Phonograph Stereoisomers: definition is based on the parts of the word. Iso = “Same/equal” Mer = “part” Stereo device Stereo = solid body that exists in three dimensions. Stereoisomers = molecules made of the same parts that exist differently in three-dimensional space. Stereo device Stereocenter = sp3 carbon atom in a molecule that has stereochemistry. Substituent = atoms that are bonded too (i.e., hanging off) an atom; especially important in defining stereoisomers. Organic Chemistry for Pharmacy: Stereoisomers: Stereoisomers: Same Parts, Same Connections, Different Arrangements in Space Two Types of Stereoisomers to Know: Geometric (sp2 hybridized alkenes) – Stereochemistry not defined by a center/point; multiple atoms create stereochemistry Optical (sp3 hybridized carbon atoms) – Stereochemistry is defined by a stereocenter Organic Chemistry for Pharmacy: Stereoisomers: Geometric (sp2 hybridized alkenes) Sp2 Hybridized Stereoisomers: Same # of atoms Exact same bonding patterns Different arrangements in 3D space Cis (Z) or Trans (E) stereoisomers possible But why, exactly, can these sp2 molecules produce stereoisomers? Organic Chemistry for Pharmacy: Stereoisomers: Geometric (sp2 hybridized alkenes) Sp2 hybridized carbons: 3 sp2 hybridized orbitals making 3 sigma bonds One non-hybridized p orbital, making the pi bond Pi bond cannot rotate; locks the substituent on the sp2 hybridized carbons into the front or back of the plane. Alkenes are different stereoisomers if the different substituents are locked on the front or back of the molecule. The presence of different substituents in different places changes the properties of the molecule. Organic Chemistry for Pharmacy: Stereoisomers: optical (sp3 hybridized carbon atoms) Asymmetric: property of lacking symmetry: having no parts that are the same as another part; a sp3 carbon atom with 4 non-identical substituents Chirality: geometric property of molecules, in which the mirror image of the molecule is non- superimposable on the molecule Achiral: geometric property of molecules, in which the mirror image of the molecule CAN be superimposed on the molecule; likely a plane of symmetry exists in the molecule. Chiral = Greek for hand. Each hand is chiral because it has a different front, back, top and bottom; no symmetry. Organic Chemistry for Pharmacy: Stereoisomers: optical (sp3 hybridized carbon atoms) Disposable glove: Front and back of these Winter glove: front and back are different; gloves are not different; asymmetric and chiral; means it is a symmetrical = achiral; Can only be used on one hand. can be used on either hand. Organic Chemistry for Pharmacy: Understanding sp3 chiral stereocenters sp3 hybridized carbon atom with 4 different substituents is: asymmetric and therefore that carbon atom is a stereocenter. A sp3 stereocenter is a chiral center (i.e., has the property of chirality). A chiral center in a molecule makes the entire molecular chiral. Organic Chemistry for Pharmacy: Understanding sp3 chiral stereocenters How many different ways can the same 4 substituents be differently arranged around a sp3 hybridized carbon? That is, how many different ways can a stereocenter exist? The way the 4 groups are bonded to the sp3 center is called the configuration. Imagine a case where 4 versions of the same molecule are drawn, but in each molecule, the yellow group switches with the green (ii), blue (iii), and red circles (iii). This drawing would indicate that there are 4 different configurations possible for the stereocenter? This would be wrong…. Organic Chemistry for Pharmacy: Understanding sp3 chiral stereocenters By rotating the molecules in space, we can determine that there are actually only two configurations for the 4 substituents to be bonded to the central sp3 atom. The two different configurations around the sp3 center are the non-superimposable mirror images of each other; the two compounds ARE NOT THE SAME COMPOUNDS! These two different molecules with the different configurations are enantiomers of each other. The two configurations for any sp3 enantiomer can be designated as either (R) or (S). Stereochemical properties of sp3 carbon atoms: Non-Superimposable Mirror Images of Molecules Chirality: geometric property of molecules, in which the mirror image of the molecule is non-superimposable on the molecule The two different configurations around the sp3 center are the non-superimposable mirror images of each other; the two compounds ARE NOT THE SAME COMPOUNDS! These two different molecules with the different configurations are enantiomers of each other. Stereochemical properties of sp3 carbon atoms: Superimposable Mirror Images of Molecules Achiral: geometric property of molecules, in which the mirror image of the molecule CAN be superimposed on the molecule; likely a plane of symmetry exists in the molecule. sp3 hybridized carbons with two identical substituents are achiral; NOT stereocenters, no stereochemistry. These two compounds (C and D) are the same compound. Stereoisomers: Definitions Based on Greek Word Roots Iso = “Same/equal” Mer = “part” dia = across or through (diameter, diagonal) Enant = opposite Enantiomer = two identical molecules that have one part (i.e. stereocenters) which are opposite from each other (R versus S stereocenters) Diastereomers = molecules made of the same parts that are different across a plane of symmetry. Enantiomers: Molecular Good/Evil Twins Two spiderman look the same, same physical characteristics Only by seeing how they act in the world can they be distinguished Two enantiomers have same overall molecular properties (i.e., polarity, molecular weight, melting point, boiling points, etc.). Designated as either (R) or (S) enantiomers, depending on the configuration at the stereocenter. The two enantiomers can only be distinguished by how they interact with external chiral molecules or chiral light. Enantiomers: Distinguishing Between Good and Evil Proteins can always tell the difference between enantiomers… As we will see, proteins are made up chiral amino acids: therefore, all proteins are chiral As chiral molecules, proteins will have different binding interactions with the different enantiomers of the same drug. example protein structure Diastereomers: Two Sets of Twins Molecules with two or more different sp3 chiral stereocenters can exist as diastereomers. Diastereomers are made of the same atoms and bonds; differ only through the configuration at the 2 or more stereocenters. Therefore, diastereomers are stereoisomers of each other. With the difference in configuration, two diastereomers are not mirror images of each; nor are two diastereomers internally the same. This means that diastereomers DO NOT have the same physical properties. A compound with 2 stereocenters can exist as a total of 4 stereoisomers: two pairs of enantiomers, with stereochemical configurations of (R,R), (S,S), (R,S) and (S,R) Racemic Molecules: Equal Parts of Each Enantiomer An equal mixture of two enantiomers (i.e., a 50/50 mixture) is called a racemic mixture (aka racemate). The existence of a racemic mixture of a molecule is indicated by the squiggly lines showing the bond between the sp3 stereocenter and its substituents. The chemistry technology required to produce most drug molecules as single enantiomers is only around 20 years old. Therefore, many older drugs are used as racemic mixtures, since a single enantiomer could not be prepared. Drugs used as racemic mixture are therefore a mixture of two different enantiomer drug molecules compounds; since proteins can distinguished between enantiomers, a racemic mixture contains two drug molecules capable of having different interactions with different proteins. The presence of the second enantiomer compound in a racemic mixture of drugs can have important pharmacological effects (e.g., thalidomide story). Molecular Introduction to Biomolecules: Universal building blocks of life All living creatures are made of the same 4 major classes of biomolecules built of 6 elements. Major Class of Biomolecules Nucleic acids (DNA & RNA) Proteins Other elements are essential for life but do Lipids not make up the 4-classes of biomolecules Carbohydrates (examples: Fe, K, Na and many others). Bacteria Fungi Plants Animals Humans The 4 different classes of biomolecules are recognized by their molecular structures; the molecule structures dictate the molecular function. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Lipids Lipids are small molecular weight (< 1000 g/mol) mainly hydrophobic molecules. Unlike the other three classes of biomolecules, lipids are not just one kind of molecule, but a miscellaneous assortment of several kinds of molecular classes. The classification of the lipid is non-specific for molecule structure; instead, it is a classification based on poor aqueous solubility. Therefore, lipid molecules can be identified based on the features of their molecular structures: 1) mainly made of non-polar bonds (C-C and C-H bonds) with a few key polar function groups 2) Unlike amino acids/proteins, nucleic acids, or carbohydrates, lipids are NOT polymers; do not make repeating units, which explains the small molecule sizes of lipids. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Lipids Lipid are a hodgepodge of molecular classes – Hodgepodge (definition) – a heterogenous mixture, a jumble Different kinds of lipids have different but somewhat related structures. Different kinds of lipids have broadly related function. Analogy of the Kitchen Utility Drawer to Lipids? Everything must fit in the drawer (not too large) Also, vaguely similar function and shape; things you use with your hands. Molecular Introduction to Biomolecules: Three Major Classes of Lipids to Know: Triglycerides/Fatty Acids Phospholipids: Steroids: Lipids are mainly made of non-polar bonds (C-C and C-H bonds) with a few key polar function groups Molecular Introduction to Biomolecules: Three Major Classes of Lipids to Know: Fatty Acids/Triglycerides Fatty Acids Fatty acids are lipids with long carbon chains and a single carboxylic acid FG. Different fatty acids differ in the length of the carbon chain (i.e., C14-C22 carbon chain length) and the number and stereochemistry of alkenes present on carbon chain (i.e., saturated vs. unsaturated). Fatty acids are used as energy storage in the cells and in the body, as well as a source for carbons to build biomolecules; very high in calories. In the body, fatty acids are almost always deprotonated to produce the anion carboxylate Therefore, the physiochemical properties of fatty acids are very long non-polar hydrocarbon chain and a very polar ionic FG at one end of the molecule. Molecular Introduction to Biomolecules: Three Major Classes of Lipids to Know: Fatty Acids/Triglycerides Triglycerides (3 fatty acids + glycerol) For long term energy storage, fatty acids can be converted into triglycerides through 3 fatty acid molecules bonding to glycerol. Esterification enzymes combine the hydroxyl of glycerol and the carboxylic acid of the fatty acid to make an ester FG. Triglyceride have different physiological properties than fatty acids; no longer charged ionic, although still polar. Molecular Introduction to Biomolecules: Three Major Classes of Lipids to Know: Phospholipids Phospholipids are similar to triglycerides, but at one of the glycerol hydroxyls a charged phosphate polar group is present. Phospholipid are made up of various fatty acids (i.e., different lengths and number of alkenes) to make a diglyceride. The phospho-containing head group means that the phospholipid is always charged, highly polar….unlike the triglycerides. Introduces a very pronounced overall difference in polarity between the polar phospho-group and the non-polar carbon tail. This strong difference in polarity allows phospholipids to spontaneously organize in water through intermolecular forces to make a lipid bilayer membrane. Molecular Introduction to Biomolecules: Three Major Classes of Lipids to Know: Phospholipids The charged, polar head group loves to interact with water through hydrogen bonds The non-polar carbon-carbon tail has no interactions with water; hydrophobic Molecular Introduction to Biomolecules: Three Major Classes of Lipids to Know: Phospholipids Lipid Bilayer; makes up cell membranes A biological problem: How to build separate compartments in a complex, aqueous system? The barriers need to be changeable and built from the inside out. Channel intermolecular forces to self-organize phospholipids to make membranes made up of a lipid bilayers Molecular Introduction to Biomolecules: Three Major Classes of Lipids to Know: Phospholipids Two intermolecular Forces building lipid bilayers 1) Hydrogen bonding between polar phospho-containing charged head groups and water molecules 2) London dispersion forces between the long, nonpolar hydrocarbon tails of adjacent phospholipid molecules Lipid bilayers are the major components of membranes. Self-organize due to physiochemical properties, like oil on top of water. Membranes are the dividers in life, providing barriers between different organelle and cells. Molecular Introduction to Biomolecules: Three Major Classes of Lipids to Know: Steroids Steroid are lipid structures made up of 4 carbon rings, fused together Different steroids have different substituents on the steroid skeleton Steroids are highly non-polar, and unlike other lipid classes, very rigid Steroid lipids have two main functions: 1) Serve as components in lipid bilayers, modulating the fluidity of the bilayer (cholesterol) 2) Serve as signaling molecules in the body (e.g., testosterone and estrogen) Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Amino Acids/Proteins Proteins are the biomolecules that provide structure and function to living systems. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Amino Acids/Proteins Anatomy of Amino Acids: Amine group Carboxylic acid group Side chain differs in each a.a. (R group) one sp3 carbon connecting amine and carboxylic acid; sp3 carbon is a stereocenter (except for the amino acid glycine) Different ends of the amino acid: Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Amino Acids/Proteins Peptides: A Biopolymer of Amino Acids: Amino acids come together (i.e., polymerize) through formation of a new FG: the amide. The amide comes from the amine from one a.a. bonding to the carboxylic acid of another amino acid. Amide are strong, sp2 hybridized FGs; can only really be broken in the body by specific enzymes. Since each amino acid is chiral with a stereocenter (except for a.a. glycine), the peptides are diastereomers. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Amino Acids/Proteins Proteins are biopolymers of amino acids bonded together. Polymer: a substance made through subunits being attached. Small number of amino acids bonded together = peptide. Many amino acids (>80 a.a.) polymerized (i.e., bonded together) = protein Proteins are the biomolecules that provide structure and function. Proteins have stereochemistry because they are built of amino acids, which have stereochemistry. Sugar = Carbohydrate; Saccharide = individual carbohydrate molecules, such as one molecule of glucose Monosaccharide = 1 carbohydrate molecule; Disaccharide = 2 carbohydrate molecules ; Polysaccharide = many carbohydrates Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Carbohydrates Carbohydrates are a class of biomolecules consisting of carbon, hydrogen and oxygen. Carbohydrate name = carbon + water. Carbohydrates have between 3 and 7 carbon atoms. One carbon atom is part of a sp2 hybridized FG; either an aldehyde (aldose) or ketone (ketose) FG. The other carbons are sp3 hybridized, often with hydroxy substituents Many carbohydrates are stereoisomers of one another: same atoms and bonding patterns between two molecules, but one stereocenter is different = diastereomers Many carbohydrates exist in an equilibrium between an open, linear form and a closed, cyclic form Need to be able to identify a carbohydrate biomolecule based on its molecular structure. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Carbohydrates Many monosaccharides are constantly opening and closing (i.e. cyclizing) Need to be able to identify a carbohydrate biomolecule based on its molecular structure. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Carbohydrates Carbohydrates have many different biological functions, but three major functions are to: 1) Serve as an energy source/energy currency in the body (e.g., glucose) 2) Serve as a medium term energy storage through making a polysaccharide (i.e., a polymer of glucose units). 3) Provide a scaffold to build nucleic acids (i.e., ribose and deoxyribose) Cyclized carbohydrates are often drawn in 3D representations (i.e., chair conformations), as shown for glucose. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Nucleic Acids Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Nucleic Acids DNA and RNA are the main nucleic acids. Nucleic acids are biopolymer molecules made of nucleotides polymerized together Nucleotides bonded through phosphate linkages forms the biopolymers DNA and RNA. What are nucleotides? Nucleotides are small molecules made of three components: nucleobase + ribose carbohydrate + phosphate molecules Nucleotides have important biological functions other than making up DNA and RNA, such as energy (ATP) and cell signaling AMP, GTP, CTP. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Nucleic Acids Mixing Different Building Blocks to Make Different Nucleotides: Either ribose or deoxyribose One of 5 nucleobase Need to be able recognize ribose and deoxyribose in both cyclized and non-cyclized forms Need to be able to recognize the 5 nucleobases; do not need to name each one. Molecular Introduction to Biomolecules: Four Major Classes of Biomolecules: Nucleic Acids Examples of nucleotides in drug molecules New polynucleotide drugs on the horizon? The Moderna and Pfizer COVID-19 vaccines use an RNA polynucleotide to make a viral protein, to trigger immunity.