Drug design: optimizing target interactions PDF

D r u g design: optimizing target interactions Chapter 13 Supervisor : profe ssor Re e m A b u ta y e h Ay a Wa h b e h - 202215101 Nada A ba bneh - 2 0 2 3 1 5 0 4 1 11/11/202 Z...

D r u g design: optimizing target interactions Chapter 13 Supervisor : profe ssor Re e m A b u ta y e h Ay a Wa h b e h - 202215101 Nada A ba bneh - 2 0 2 3 1 5 0 4 1 11/11/202 Z a i d Alkhalaileh - 1 4 Outline 13.1 Structure–activity relationships 13.2 Identifi cation o f a pharmacophore 13.2 Identifi cation o f a pharmacophore 11/11/202 2 4  13. 1 Stru ctu re–activity relationships Structure–activity relationships (SAR): The aim is to identify those parts of the molecule that are important to biological activity and those that are not. 11/11/202 3 4  One can imagine the drug as a chemical knight entering the body to make battle with an affliction. Th e drug is armed with a variety of weapons and armour, but it may not be obvious which weapons are important to the drug’s activity, or which armour is essential to its survival. We can only find this out by removing some of the weapons and armour to see if the drug is still effective. Let us consider the binding interactions that are possible for different functional groups and 11/11/202 4 the analogues that could be synthesized to 4  13.1.1 Binding role o f alcohols a n d phenols Alcohols and phenols are functional groups which are commonly present in drugs and are often involved in hydrogen bonding. The oxygen can act as a hydrogen bond acceptor, and the hydrogen can act as a hydrogen bond donor. The reason why the ether might hinder or prevent the hydrogen bonding of the original alcohol or phenol. The obvious explanation is that the proton of the original hydroxyl group is involved as a 11/11/202 hydrogen bond donor 5 4  3.1.2 Binding role o f a ro m atic rings Aromatic rings are planar, hydrophobic structures, commonly involved in van der Waals interactions with flat hydrophobic regions of the binding site. The binding region for the aromatic ring may also be a narrow slot rather than a planar surface. 11/11/202 6 4  13.1.3 Binding role o f alkenes Like aromatic rings, alkenes are planar and hydrophobic so they too can interact with hydrophobic regions of the binding site through van der Waals interactions. 11/11/202 7 4  13.1.4 The binding role o f ke t o n e s a n d aldehydes A ketone group is not uncommon in many of the structures studied in medicinal chemistry. It is a planar group that can interact with a binding site through hydrogen bonding where the carbonyl oxygen acts as a hydrogen bond acceptor Aldehydes are less common in drugs because they are more reactive and are susceptible to metabolic oxidation to carboxylic acids. However, 4 they could interact in the same way 11/11/202 8  13.1.5 Binding role o f Amines areamin extremelyes important functional groups in medicinal chemistry and are present in many drugs. They may be involved in hydrogen bonding, either as a hydrogen bond acceptor or a hydrogen bond donor. The nitrogen atom has one lone pair of electrons and can act as a hydrogen bond acceptor for one hydrogen bond. Primary and secondary amines have N–H groups and can act as hydrogen bond donors. Aromatic and heteroaromatic amines act only as 11/11/202 9 4  13.1.6 Binding role o f amides Many of the lead compounds currently studied in medicinal chemistry are peptides or polypeptides consisting of amino acids linked together by peptide or amide bonds. Amides are likely to interact with binding sites through hydrogen bonding. The most common type of amide in peptide lead compounds is the secondary amid. 11/11/202 10 4  Amides which are within a ring system are called lactams. If the ring is small and suffers ring strain, the lactam can undergo a chemical reaction with the target leading to the formation of a covalent bond. 11/11/202 4 11  13.1.7 Binding role o f quaternary a m m o n i u m salts Quaternary ammonium salts are ionized and can interact with carboxylate groups by ionic interactions. Another possibility is an induced dipole interaction between the quaternary ammonium ion and any aromatic rings in the binding site. Example: The neurotransmitter acetylcholine has a quaternary ammonium group which is thought to 11/11/202 12 4  Nada Ababneh 13.1 Structure–activity 20231504 1 relationships 8. Binding role of carboxylic acids 9. Binding role of esters 10. Binding role of alkyl and aryl halides 11. Binding role of thiols and ethers 12. Binding role of other functional groups 13. Binding role of alkyl groups and the carbon skeleton 14. Binding role of heterocycles 15. Isosteres 16. Testing procedures 17. SAR in drug optimization 13.2 Identifi cation o f a pharmacophore 11/11/202 13 4  13.1.8 Binding role o f carboxylic acids The carboxylic acid group is common in drugs and can act as a hydrogen bond acceptor or donor. It may exist as the carboxylate ion which can acts as the hydrogen bond acceptor. This allows the possibility of an ionic interaction and /or a strong hydrogen bond. 11/11/202 14 4  13.1.8 Binding role o f carboxylic acids To test the possibility of such interactions, analogues such as : esters, primary amides, primary alcohols, and ketones could be synthesized and tested. None of these functional groups can ionize, so a loss of activity could imply that an ionic bond is important. 11/11/202 15 4 11/11/202 16 4  13.1.9 Binding role o f esters An ester functional group has the potential to interact with a binding site as a hydrogen bond acceptor only. Carbonyl oxygen it is sterically less hindered and has a greater electron density. 11/11/202 17 4  13.1.9 Binding role o f esters Esters are susceptible to hydrolysis in vivo by metabolic enzymes called esterase. This may a problem if the lead compound contains an ester that is important to binding , might the drug have a short lifetime in vivo. Several drugs that do contain esters and are relatively stable to metabolism thanks to electronic factors that stabilize the ester or steric factors that protect it. 11/11/202 18 4  13.1.9 Binding role o f esters Esters that are susceptible to metabolic hydrolysis are sometimes used deliberately to mask a polar functional group. such as a carboxylic acid, alcohol, or better from phenol, to achieve absorption the gastrointestinal tract. Once in the blood , the ester is hydrolyzed to release the active drug. This is known as a prodrug strategy. 11/11/202 19 4 11/11/202 20 4  13.1.10 Binding role o f alkyl a n d aryl halides Alkyl halides involving chlorine, bromine, or tend to be chemically reactive iodine as the halide ion is a good leaving group. Drug containing an alkyl halide is likely to react with any nucleophilic group that it encounters and become permanently linked to that group by a covalent bond. 11/11/202 21 4  13.1.10 Binding role o f alkyl a n d aryl halides Alkyl fluorides, not alkylating agents , because are strong and resistant to breaking due to their C-F bond. Commonly used to replace a proton for two reason: I. It is approximately the same size has different electronic properties. II. Protect the molecule from metabolism. 11/11/202 C-F > C-CL > C-Br > C- 22 4  13.1.10 Binding role o f alkyl a n d aryl halides As the halogen substituents are electron-withdrawing groups, electronthey density affect influen of the aromatic ring, and this may have an on the binding of the aromatic ring. ce 11/11/202 23 4  13.1.11 Binding role o f thiols a n d ethers The thiol functional group (S–H) is recognized as an effective ligand for d-block metal ions and has been integrated into numerous pharmaceutical agents engineered to metalloprotein inhibit enzymes that possess a zinc cofactor, such as zinc ases If the lead compound has a thiol group, the corresponding alcohol could be tested as a comparison. This would weaker interaction with zinc. 11/11/202 24 4 11/11/202 25 4  13.1.11 Binding role o f thiols a n d ethers An ether group act as a hydrogen bond oxyge ato acceptor through the n m. This could be tested by increasing the size of the alkyl group to see whether it diminishes the ability of the group to take part in hydrogen bonding. Analogues where the oxygen is replaced with a methylene isostere should show significantly decreased binding affinity. 11/11/202 26 4  13.1.12 Binding role o f other functional gro u p s A wide variety of other functional groups may be present in lead compounds hav no directthat binding role but could be important in e other respects. I. Influence the electronic properties of the molecule (e.g., nitro groups or nitriles). II.Restrict the shape or conformation of a Functional groups may also act as metabolic blockers molecule (e.g., (e.g., aryl alkynes) III. halides) 11/11/202 27 4  alkyn es nitro g ro u p s nitril aryl halides 24 es 11/11/20 2 8  13.1.13 Binding role o f alkyl g ro u p s a n d the carbon skeleton The alkyl substituents and carbon skeleton of a lead hydropho compound are with hydrophobic regions of the bindingbic and may bind site through van der Waals interactions. If the alkyl is linked to nitrogen or oxygen, it may be possible removal lead compound may group reduc its activity if it's involved in significant from a hydrophobic e interactions. The analogues may have less activity if the alkyl group was involved in important hydrophobic interactions. 11/11/202 29 4 11/11/202 30 4  13.1.14 Binding role o f heterocycles Heterocycles are cyclic structures that contain one or more heteroatoms , commonly occurring heteroatom is nitrogen followed by oxygen and Sulphur. The heterocycles can classification of Heterocyclic Compounds , aliphatic or aromatic in character and have the potential to interact with binding sites through a variety of bonding forces. Individual heteroatoms present in the structure could interact by hydrogen bonding or ionic bonding. 11/11/202 31 4 11/11/202 32 4  The ideal direction for those interaction 11/11/202 33 4  13.1.14 Binding role o f heterocycles Tautomer : the type of isomerism which arise due to shifting of proton within a molecule. Watson and Crick originally tried to devise a model for DNA, they incorrectly assumed that the preferred tautomer for the nucleic acid bases were as shown in the 11/11/202 34 4  13.1.15 Isosteres Isoster are atoms or groups of atoms which share the same es have chemical valency,orand physical which similarities. 11/11/202 36 4  13.1.15 Isosteres Isosteres can be used to determine whether a particular group is an important binding group or not , by altering the character of the molecule in as controlled a way as possible. Replacing O with CH2 makes little difference to the size of the analogue, but will have a marked effect on its polarity, electronic distribution, and bonding. Replacing OH with the larger SH may not have such an influence on the electronic character, but steric factors become more significant. 11/11/202 37 4  13.1.15 Isosteres β-blocker propranolol ReplacementOCH of the with isosteres 2 theCH = CH , SCH2 , eliminates activity.CH2 CH2 Whereas NHCH retains replacement with 2 activity. These results show that the ether oxygen is important to the activity of the drug and suggests that it is involved in hydrogen bonding with the receptor. 11/11/202 38 4  13.1.16 Testing procedures Biological testing should investigate the structure-activity relationships for drug- target binding interactions. In vitro tests, such as inhibition studies on enzymes or binding studies on membrane-bound receptors in whole cells, determine the crucial binding groups in drug-target interactions. In vivo , testing is carried out the results are less clear-cut because loss of activity. 11/11/202 39 4  13.1.16 Testing procedures In vivo testing may reveal functional groups that are important in protecting or assisting the drug in its passage through the body. Th is would not be revealed by in vitro testing. NMR spectroscopy can also be used to test structure activity relationships. 11/11/202 40 4  13.1.17 S A R in d r u g optimization we have focused on SAR studies aimed at identifying important binding groups in a lead compound. SAR studies are also used in drug optimization, where the aim is to find analogues with better activity and selectivity. This involves further modifications of the lead compound to identify whether these are beneficial or detrimental to activity. 11/11/202 41 4 13.2 I 0den2tification o f a ph a rm a c o p h o re  Identifying important drug groups is the next stage after determining the drug's activity. Pharmacophore : the important binding groups that are required for activity, and their relative positions in space with respect to each other. Important binding groups for drug glipine are the two phenol groups, the aromatic ring, and the nitrogen atom. Structure two- 11/11/202 43 4  Specifies the relative positions of the important groups in space. It is not necessary to show the specific skeleton connecting the important groups. Indeed, there are benefits in not doing so, as it is easier to compare the 3D pharmacophores from different structural classes of compound to see if they share a common pharmacophore. Once a 3D model of a structure has been constructed, it is a straightforward procedure to measure all its bond lengths, bond angles. 11/11/202 Structure Three- 44 4  Molecule can adopt many conformations which place the important binding groups in different positions relative to each other Normally, only one of these conformations is recognized and bound by the binding site. This known as the active conformation. To identify the 3D pharmacophore, it is necessary to know the active conformation. 11/11/202 45 4  X-ray crystallography could then be used to identify the structure of the complex, as well as the active conformation of the bound ligand and is to obtain a three-dimensional molecular structure from a crystal. Progress has been made in using NMR spectroscopy to solve the active conformation of isotopically labelled molecules bound to their binding sites. 11/11/202 46 4  0 1 3. 3 D r u g Optimization: Strategies in D r u g Design 3 Prepared by: Z a i d Alkhalaileh, P h a rm D Supe rvi se d by: Dr. Re e m A b u Taye h Le a d Optimization in D r u g Design W h y Optimize?  Le a d c o m p o u n d s o ft en h a v e limitations (low activity, po or selectivity, side eff ects). Optimization Goals: Increase Po t e n c y (stronger t a rget interaction). Impro ve A D M E (better absorption, distribution, metabolism, excretion). Balance Solubility (water a n d lipid). Redu ce Toxicity (safer profile). Result: Impro ved a n a l o g u es w i t h higher effi cacy, selectivity, and ea s11/11/20 e o f synthesis. 4 24 8  Lead Optimization  Once the important binding groups and pharmacophore of the lead compound have been identified, it is possible to synthesize analogues that contain the same pharmacophore. 1. Variation of aliphatic substituents (A. Chain extension/contraction + B. chain branching ) 2. Extension of the whole structure 3. Variation of aromatic substituents (change position just) 4. Ring expansion/contraction 5. Ring variations 6. Ring fusion 7. Isosteres and bioisosteres 8. Simplification of the structure 49  1. Variation of aliphatic A. substituents Homologation (Chain extension/contraction ) : def  Extension or contraction of the carbon chain length. (linker) Increasing or decreasing compounds by a constant unit (e.g., CH₂), which can either improve or reduce binding interactions. B. Chain branching : Adding branches to the main carbon chain. 11/11/202 50 4  1.A Homologation (Chain  Some drugs have Extension/Contraction) two important binding groups (pharmacophore groups) linked together by a chain. In such cases, the chain length may not be ideal for optimal interaction.  Pharmacophore vs. Auxophore: Pharmacophore: The essential part of the molecule responsible for biological activity. Auxophore: The "rest of the molecule" that may not directly interact with the target but affect on the pharmacophore. 11/11/202 51 4  1.A Homologation (Chain  Extension/Contraction) Example: N-Phenethylmorphine  Modification: Derived from morphine by replacing the N-methyl group with a β-phenethyl group.  Effect on Potency: This modification makes N-Phenethylmorphine approximately eight to fourteen times more potent than morphine.  Chain Length Influence: When the chain length is 1 or 3, the potency decreases significantly. 11/11/202 52 4  1.A Homologation (Chain  Extension/Contraction) Vary length and bulk (next slide) of alkyl group to introduce selectivity.  Receptor families often have multiple subtypes with slight structural differences, such as binding pocket depth, width, or length.  Ex, seen in receptors like dopamine (D1, D2, D3) and serotonin (5-HT1A, 5-HT2A) 11/11/202 53 4  1.B Chain  branching Vary length (previous slide) and bulk of alkyl group to introduce selectivity.  Selective Binding with Larger Alkyl Groups: Concept: Adding bulkier alkyl groups can increase selectivity by blocking binding to certain receptors, reducing side effects. Example: Salbutamol (Ventolin / anti-asthmatic / bronchodilator ), a modified form of adrenaline (α + β ), replaces a methyl group with a tert-butyl group, creating selectivity for β.2-adrenergic receptors over α-adrenergic receptors. adrenaline (α adrenaline (α Salbutamol +β) +β) β.2 11/11/202 54 4  2. Extension of the whole  structure Extension Strategy: Involves adding a new extra functional group to the lead compound.  Commonly used to convert an agonist into an antagonist by adding hydrophobic interactions.   Increased hydrophobicity makes the compound Rate Theory and Pharmacological Activity: "stickier," enhancing rat of association and dissociation between drug antagonist behavior. Based on the e and receptor. 1.Agonists: Fast association and dissociation rates → frequent receptor activation. Small, lean molecules. 2.Antagonists: Fast association but slow dissociation → prolonged binding without activation. Large, lipophilic molecules, forming strong Van der Waals and hydrophobic interactions. 11/11/202 55 4  2. Extension of the whole structure, example.1+2  Propranolol: structural modifications, including a benzene ring, oxygen, and propyl increase group  hydrophobicity and binding stability, selective for β- making it receptors to lower heart rate and treat high blood 3. pressure. Benzene  Cimetidine: structural modifications, including a sulfur atom and an imidine- enhances amidine group "stickiness, hydrophobicity " to effectively block allowing it histamine’s action on H₂ receptors, reducing stomach acid. 11/11/202 56 4  2. Extensi on o f the example whole structure.3 , 11/11/20 5 24 7  3. Variation of aromatic  The substituents of substituent groups on an aromatic ring (e.g., para vs. position meta) can affect binding interactions. Adjusting the substituent position can lead to stronger or weaker binding, depending on alignment with the target's binding site.  Example: Moving an -OH group from a para to a meta position: - Meta position: Allows stronger hydrogen bonding with the binding site, increasing binding affinity. - Para position: May result in weaker binding if it doesn’t align well with the binding site. - Result: Optimizing substituent positions on the aromatic ring can enhance drug activity Does and effectiveness. the binding pocket act as a Hydrogen Bond Donor (HBD) or a Hydrogen Bond Acceptor (HBA) for the -OH group in the molecule ? 11/11/202 58 4  4. Ring  Definition: When aexpansion/contraction drug contains rings essential for binding, modifying the ring size by expanding or contracting it can improve binding interactions  Then adjusts the spatial orientation, potentially achieving better alignment with regions in the binding site. Example Expanding a from.1 ring : t 5-membereda o 7-membered improved alignment, positioning each functional group for optimal interaction with the binding pocket, enhancing binding affinity. 11/11/202 59 4  4. Ring expansion/contraction  (Example.2) In the development of Cilazapril (an ACE inhibitor), ring expansion was used to improve binding within the active site.  Expanding the ring affected two key factors  1.Distance / 2.Orientation.  Key Binding Interactions Achieved by ring expansion  1.Stronger Hydrogen Bonding / 2. Stronger Ionic Interaction / 3.New Ionic Interaction. 11/11/202 60 4  5. Ring variations  (Example.1) Concept: Replacing an aromatic or heteroaromatic ring in drug molecules with alternative rings of different sizes or heteroatom positions is a common strategy in drug design. Aims to improve potency , selectivity, and reduce side effects. 4. amide 11/11/202 61 4  5. Ring variations  (Example.2) Imidazole vs. 1,2,4-Triazole in Antifungal Drugs. A. Imidazole Ring (Original Structure): Mechanism: Inhibits fungal enzymes involved in ergosterol synthesis, which is essential for fungal cell membrane integrity. Drawback: Lacks selectivity; also inhibits similar human enzymes involved in cholesterol synthesis, causing side effects like liver toxicity and hormonal imbalances. B. 1,2,4-Triazole Ring (Modified Structure - UK 46245): Mechanism: Improved selectivity for fungal enzymes over human Enzymes. 11/11/202 62 4  5. Ring variations  (Example.3) Example in Antivirals: Structure I (the lead compound in an antiviral replacing an aromatic ring project) was modified by with a pyridine which introduced a new hydrogen bond acceptor with the ring, target enzyme.  Further optimization of this structure led to the development of the antiviral agent nevirapine (to treat and prevent HIV/AIDS). 11/11/202 63 4  6. Ring fusion  Replacing adrenaline’s aromatic ring with a naphthalene ring (in selectiv for β- pronethalol) enhanced ity receptors byincreasing van der Waals and fitting the larger β-receptor interactions binding area. 3. Naphthalen e 11/11/202 64 4  7. Isosteres and Bioisosteres in  Drug Isosteres: Groups used Design to modify a molecule’s features (size, polarity, electronic properties) to study activity and stability.  Bioisosteres: Isosteres specifically retain biological while replacing problematic chosen to activity functional groups.  Purpose: 1. Modify size or electronic without changing distribution activity. 2. Improve selectivity, reduce toxicity, or enhance binding interactions. Example.1: Fluorine can replace hydrogen to increase electronegativity (both Same size)  as seen in 5-fluorouracil, which disrupts enzyme activity by mimicking uracil. 11/11/202 65 4  7. Isosteres and Bioisosteres in Drug Design  (Example.2) Using bioisosteres to replace thiourea in drug design provides several key benefits cyano- 1. Reduced Toxicity: Bioisosteres like or nitro- replace toxic thiourea, making the drug guanidine guanidine safer for long-term use. 2. Preserved Activity: Bioisosteres cyano- like nitrog- are carefully chosen because and guanidine uanidine they have similar basicity (tendency to accept protons) and planar geometry of thiourea 3. Enhanced Selectivity: In some cases, the bioisostere may even introduce additional interactions (e.g., hydrogen bonding), which can improve the binding strength and specificity of the drug. 11/11/202 66 4  7. Isosteres and Bioisosteres in Drug Design (Example.3)  Psychosis and Dopamine Receptors antagonist : Psychosis: A mental disorder characterized by losing touch with reality, such as hallucinations and delusions. Dopamine Receptors: 1. D2 Receptor: Involved in motor control. Blocking it can lead to extrapyramidal symptoms (EPS) like tremors and rigidity. 2. D3 Receptor: Involved in mood and cognition, causing fewer motor side effects when targeted. ( our target ) 11/11/202 67 4  7. Isosteres and Bioisosteres, Continued to Example.3 Challenge with Traditional Older antipsychotics not selective so bind to D3 receptor, Drugs: which can control psychotic symptoms but often causes movement-related side effects (EPS) related to D2 binding. Bioisosteric Design in Sultopride: 1. Bioisostere Use: By replacing an amide group with a pyrrole ring (a non-classical bioisostere), sultopride was redesigned to selectively target the D3 receptor. 2. Result: Increased selectivity for D3 over D2 receptor means effective treatment of psychosis with reduced side effects. 11/11/202 68 4  8. Simplification of the  Simplification is structure a key strategy in optimizing lead compounds from natural sources, primarily to enhance synthesizability, reduce toxicity, and improve pharmacokinetic properties.  Key Aspects of Simplification: 1.Identifying Essential Groups: By applying structure-activity relationship (SAR) techniques, essential pharmacophoric groups are identified and retained while non-essential parts are discarded to maintain activity with a simpler structure. Simplification often involves removing unnecessary simplifying the carbon (e.g., 2.Reducing Complexity: skeleton functional groups, ring removal), and eliminating asymmetric centers which complicate synthesis. (chiral center ) 11/11/202 69 4  8. Simplification of the  Advantages of structure Simplification: Easier Synthesis: Simpler structures are easier, quicker, and cheaper to synthesize. Reduced Side Effects: Elimination of unnecessary functional groups can decrease interactions with unintended targets. Improved Drug Development Efficiency: Simplified molecules simplify the development process, from synthesis to clinical trials.  Potential disadvantages: Oversimplification Risks: Excessive simplification can lead to reduced efficacy, selectivity, and potentially increased side effects due to increased molecular flexibility and altered binding characteristics. 11/11/202 70 4  8. Simplifi cation o f the st r uc t ure (Examples) 11/11/20 7 24 1  8. Simplifi cation o f th e structure (Examples) 11/11/20 7 24 2 8. Simplifi cation o f the structure (Examples) (Stage s ) 11/11/2024 73 8. Simplifi cation o f the str uc ture (Examples) (chiralit y)  9. Rigidification of the structure (most Forms Simple and Flexible Structure difficult) billions of conformers ( Includes both bioactive and non- bioactive conformations. Can fit several targets due to variable side when binding unintended conformations  Leads to effects receptors. Binding to Desired Target  Requires fix a single, bioactive conformation  Need high entropic cost to stabilize in bioactive conformation  Decreases the molecule’s potency and activity. 11/11/202 75 4  9. Rigidification of the structure  (most difficult) Benefits of Conformationally-Rigid Structures: Increases Activity: If the bioactive conformation is a high-energy conformation, making the structure conformationally rigid ensures it is always in its bioactive form, enhancing potency significantly. Increases Selectivity: Conformational constraints help differentiate the desired target from other proteins, improving the specificity of the drug. Increases Absorption: Fewer rotatable bonds in a rigid structure can increase absorption from the gastrointestinal tract after oral administration, thereby increasing oral bioavailability.  Disadvanta ges: Increased Complexity: The molecule may become more complex and could be more difficult to synthesize, potentially increasing production costs and complicating manufacturing processes. 11/11/202 76 4  9. Rigidification of the structure (most difficult)  Methods of Rigidification 1. Introduction of Rings: Converting flexible structures into ring systems or macrocycles to lock the drug in its active conformation. (to introduce selective and more potent compound) 11/11/202 77 4  9. Rigidificatio  Another example of macrocycles : n The transformation of an acyclic pentapeptide into a more effective macrocyclic by linking critical residues to form a stable ring structure. 11/11/202 78 4  9. Rigidifi cation o f the structure (most diffi cult) 2. Introduction o f double bonds, rings, triple bonds, a n d amide groups. 11/11/20 7 24 9  9. 3. Steric blocker: Rigidificatio nused to rigidify a molecule in the traditional sense; instead, they reduce Steric blockers are not the formation of different conformers by preventing the overlap of electron clouds between two atoms. Impossible to form Impossible to 11/11/202 form 80 4  9. 3. Steric blocker: Rigidificatio nused to rigidify a molecule in the traditional sense; instead, they reduce Steric blockers are not the formation of different conformers by preventing the overlap of electron clouds between two atoms. Impossible to form Impossible to 11/11/202 form 81 4 9. Rigidifi 3. Steric cation Impossible to blocker: form 11/11/20 24  Thank you Any Questions ? Font Title: Biome light ( heading ) Text: Calibri light  Reference An_Introduction_to_Medicinal_Che mistry_ 11/11/202 84 4 Drug Design: optimizing Access to the target Chapter 17 1- Optimizing hydrophilic/hydrophobic properties The hydrophilic/hydrophobic nature of a drug affects its solubility, absorption, distribution, metabolism, and excretion (ADME). Impact oh Hydrophilicity & lipophilicity Impact of hydrophilicity Impact oh Hydrophobicity decrease absorption Poor solubility Plasma protein binding Form toxic metabolites phase II conjugation Need for desolvation (removal of water molecules) which would require additional energy. Rapid excretion  Partition Coefficient (P): The relative distribution of the drug between the two layers is quantified by the partition coefficient (P). P = [drug in n-octanol] / [drug in water].  Hydrophobic compounds have a high P value  Hydrophilic compounds have a low P value  Experimental Methods for Measuring Log P: 1 High-performance liquid chromatography (HPLC) can be used to determine log P. 2 Clog P values: Log P values can also be calculated for a given structure using software programs. These are called Clog P values to differentiate them from experimentally determined log P values  The distribution of both ionized and un-ionized species is measured by log D.  Altering Hydrophilic/Hydrophobic Balance is often approached using quantitative  Masking polar functional groups to decrease polarity Examples of Masking:  An alcohol or phenol can be converted to an ether or ester.  A carboxylic acid can be converted to an ester or amide.  Primary and secondary amines can be converted to amide or secondary/tertiary amines.  Problem of masking: Masking these groups could decrease binding interactions and lower drug activity.  Solution : temporary Masking: In some cases, it is useful to mask polar groups temporarily. The mask can be removed after absorption, allowing the drug to regain its full binding ability. Another approach is the addition of Alkyl Groups since the alkyl groups reduce polarity. Varying hydrophobic substituents to vary polarity Increasing Hydrophobicity:  Adding extra alkyl groups within the carbon skeleton can increase hydrophobicity (if the synthetic route allows).  Replacing smaller alkyl groups with larger alkyl groups can also increase hydrophobicity.  Methylene Shuffle: refers to the strategy of increasing the size of one alkyl group while decreasing the size of another.  Adding Halogen Substituents:(e.g., chloro, fluoro) can increase hydrophobicity, Bromo substituents are used less commonly but also contribute to hydrophobicity.  By adding larger alkyl groups (like methyl groups, CH₃) or shifting the positions of methylene groups in the alkyl chain (e.g., replacing a CH₂ group with a CH₃ group), the molecule becomes more hydrophobic, meaning it has a greater tendency to interact with lipid membranes and is more insoluble in water. Reference: Patrick An Introduction to Medicinal Chemistry 3/e Chapter 11 Rosuvastati n Adding or removing polar functional groups to vary polarity Variation of N-alkyl substituents to vary pKa N-alkyl groups on a drug can influence the pKa.  Larger or extra N-alkyl groups tend to have an electron- donating effect, which increases basicity (raises the pKa).  However, increasing the size or number of alkyl groups also adds steric bulk around the nitrogen atom, which hinders water molecules from solvating the ionized form, thus decreasing basicity (lowering the pKa).  This creates a balance of opposing effects—  Ring Incorporation to Modify Basicity: A strategy to reduce basicity is to incorporate a basic nitrogen group within a ring structure. Example: Benzamidine has anti- thrombotic activity but is too basic for effective absorption. Incorporating the amidine group into an isoquinoline ring (e.g., PRO 3112) reduced its basicity and increased Variation of aromatic substituents to vary pKa The pKa of an aromatic amine or carboxylic acid can be varied by adding electron-donating or electron- withdrawing substituents to the ring. The position of the substituent relative to the amine or carboxylic acid is important if the substituent interacts with the ring through resonance. Bio-isosteres for polar groups Pharmacokinetic Challenges: A carboxylic acid group is highly polar and can ionize, which may hinder drug absorption. Another strategy is using bio-isosteres can replace the carboxylic acid group while retaining similar physicochemical properties, but with improved drug absorption like 5-Substituted Tetrazole Advantages of Tetrazole: contains an acidic proton and is ionized at pH 7.4, like carboxylic acids It has a planar structure like carboxylic acids. The tetrazole anion is 10 times more lipophilic than the carboxylate anion. This increased lipophilicity improves drug absorption compared to a carboxylic acid group. Tetrazoles are resistant to many metabolic reactions that typically affect carboxylic acids. N-Acylsulphonamides as Bioisosteres: N-Acylsulphonamides have also been used as bioisosteres  Phenol Groups and Metabolic Conjugation: Phenol groups are commonly found in drugs but are susceptible to metabolic conjugation reactions (e.g., glucuronidation). Bioisosteres for Phenols: Various bioisosteres involving amides, sulphonamides, or heterocyclic rings have been used where an N–H group mimics the phenol O–H group, improving stability and reducing metabolic susceptibility.  Steric shields Susceptibility to Degradation:  Some functional groups are more prone to chemical and enzymatic degradation than others.  Esters and amides are particularly vulnerable to hydrolysis, a reaction where water breaks down the bond. Strategy to Protect Functional Groups:  A common approach to protect these vulnerable groups is to use steric shields.  Steric shields are designed to hinder the approach of nucleophiles (electron-rich species that attack electrophilic centers) or enzymes to the susceptible functional group. How Steric Shields Work:  Steric shields often involve adding a bulky alkyl group near the functional group. Steric Shields in Drug Design: Methicillin  Steric shields are used in drug design to protect certain bonds or Electronic effects of bioisosteres Another popular tactic used to protect a labile functional group is to stabilize the group electronically using a bio-isostere. 1.Stabilization via Substitution (Ester to Urethane): Replacing the methyl group of an ethanoate ester with an NH₂ group results in a urethane functional group. The urethane is more stable than the original ester, primarily because the NH₂ group (amino group) has different electronic properties. The NH₂ group feeds electrons into the carboxyl group, stabilizing it and making it less prone to hydrolysis (breakdown by water). Example: 2. Stabilization via Amide Ester groups can also be replaced with amide Substitution: groups (where NH replaces O). Amides are more resistant to chemical hydrolysis than esters. This is because the lone pair of electrons on the nitrogen in the amide donates electron density to the carbonyl group, reducing its electrophilicity and making it less reactive to nucleophiles like water. 3- Bioisosteres in Medicinal Chemistry: Bioisosteres are different from isosteres. For example, a pyrrole ring can replace an amide bond in some drugs (e.g., Du 122290, a dopamine antagonist from sultopride), and thiazolyl rings can replace pyridine rings in Ritonavir drugs like ritonavir. 4.Using Inductive Effects to Increase Stability: Electron-withdrawing groups (e.g., halogens, nitro groups) can be incorporated into molecules to increase the stability of labile (unstable) functional groups. These electron-withdrawing groups have an inductive effect that makes the molecule less reactive and helps it resist acid hydrolysis. Example: Penicillins are modified with electron- withdrawing groups on their side chains to improve resistance to acid hydrolysis. 5.Inductive Effects on Prodrug Hydrolysis: The inductive effect of groups can also influence how easily ester prodrugs are hydrolyzed in the body, impacting their  Steric and electronic modifications Steric hindrance and electronic stabilization are often used together to stabilize labile groups. Example: Procaine is a local anesthetic with an ester group, which is quickly hydrolyzed (broken down by water).This rapid hydrolysis is why procaine has a short duration of action.  Changing the ester Modification group in procaine to a less reactive to Lidocaine: amide group reduces the compound's susceptibility to hydrolysis, making the drug more stable and longer- lasting. Oxacillin  Additionally, two ortho-methyl groups on the aromatic ring of lidocaine provide steric shielding to the carbonyl group, preventing it from being attacked by nucleophiles or enzymes.  These modifications result in lidocaine, a longer-acting local anesthetic compared to procaine. Other Successful Examples: Bethanechol  Oxacillin (a penicillin antibiotic) and bethanechol (a drug used to treat urinary retention) are additional examples where steric and electronic modifications have been successfully used to enhance stability and drug effectiveness. Metabolic blockers Some drugs are metabolized through the introduction of polar groups at specific positions in their chemical structure. For example, steroids can undergo oxidation at position 6 of their tetracyclic ring, introducing a polar hydroxyl group (–OH) makes the steroid more polar, which allows it to form polar conjugates (such as glucuronides or sulfates).These conjugates are more easily eliminated from the body, as they are more water-soluble and can be excreted in urine. Introducing a methyl group at position 6 blocks the oxidation process, preventing the addition of the hydroxyl group. This modification prolongs the steroid's activity, as it slows down the metabolism and elimination of the drug. Example: Megestrol acetate, an oral contraceptive, contains a 6-. Protecting Aromatic Rings from A common strategy to protect aromatic rings (e.g., in drugs with benzene Metabolism: rings) from metabolism at the para-position is to introduce an electron-withdrawing substituent, such as a fluoro group. This modification helps prevent the aromatic ring from undergoing metabolism, which could otherwise lead to rapid drug clearance. Example: CGP 52411 is an enzyme inhibitor that acts on the kinase-active site of the epidermal growth factor receptor (EGFR). CGP 53353 (an anticancer agent) was found to undergo oxidative metabolism at the para- position of the aromatic rings. Fluoro-substituents were added to CGP 53353 to block this metabolism, helping the drug to remain active longer in the body This strategy of using fluorine has also been applied successfully in the design of gefitinib, an EGFR inhibitor used in cancer treatment.  Removal or replacement of susceptible metabolic groups Methyl groups on aromatic rings are often oxidized to form carboxylic acids, which are then quickly eliminated.  Example: Tolbutamide and Chlorpropamide: Tolbutamide, an antidiabetic drug, has an aromatic methyl substituent that is metabolized to a carboxylic acid, shortening its duration of action. By replacing the methyl group with a chloro substituent, the resulting compound, chlorpropamide, is much longer-lasting because it is less susceptible to oxidation.  Example: Cephalosporins: In the case of cephalosporins (a class of antibiotics), a susceptible ester group is often replaced with metabolically stable groups to increase the drug's stability and effectiveness.  Group shifts If a metabolically vulnerable group is crucial for binding interactions with the drug’s target (e.g., receptor or enzyme), then simply removing or replacing it isn't a viable option. In such cases, other strategies must be used to protect or modify the group without disrupting its binding affinity. Two Possible Solutions: Prodrug Strategy: Shifting the Vulnerable Group  Example: Salbutamol: Salbutamol is an analogue of the neurotransmitter noradrenaline and has a catechol structure containing two ortho-phenolic groups. One issue with catechol compounds is that they are often methylated at one of the phenolic groups by metabolic enzymes, making the compound inactive. Methylation of the phenolic groups disrupts hydrogen bonding with the receptor, thus deactivating the compound. Removing the hydroxyl group or replacing it with a methyl group would prevent the drug from being metabolized, but it would also prevent essential hydrogen bonding with the binding site, reducing the drug's effectiveness.  A hydroxyethyl group (–CH₂OH) was found to be acceptable in place of the original hydroxyl group (– OH) for effective binding. However, beyond a certain distance or size, activity is lost because the hydroxyl group would either be out of range or the substituent would be too large to fit into the receptor’s binding site.  Ring variation and ring substituents Certain ring systems in drugs are susceptible to metabolism, and modifying the ring structure can improve the drug’s metabolic stability. One approach to enhancing stability is to introduce nitrogen into the ring. This lowers the electron density of the ring system, making it less reactive to metabolic enzymes.  Example: Imidazole vs. Triazole: The imidazole ring in tioconazole (an antifungal agent) is susceptible to metabolism. Replacing it with a 1,2,4-triazole ring, as in fluconazole, results in improved metabolic stability and thereby increasing its effectiveness. Electron-Rich Aromatic Rings like phenyl groups, are particularly vulnerable to oxidative metabolism. To stabilize these rings, they can be replaced with nitrogen-containing heterocyclic rings, such as pyridine or pyrimidine, which are less prone to metabolism. Electron-withdrawing substituents (like fluorine or nitro groups) can also be added to the aromatic ring to lower electron density, reducing its susceptibility to metabolism.  Methyl groups on aromatic or heteroaromatic rings can be metabolized, but sometimes they are necessary for binding affinity and must be retained. In such cases, introducing nitrogen into the aromatic or heteroaromatic ring can be beneficial. The nitrogen lowers the electron density, which helps make the methyl group more resistant to oxidation and metabolism.  Example: F13640 and F15599: F13640 (an analgesic) underwent clinical trials, but its methyl group on the pyridine ring was susceptible to oxidation, converting it to an inactive carboxylic acid. Since the methyl group was important for binding, the solution was to replace the pyridine ring with a pyrimidine ring, resulting in F15599. F15599 had increased metabolic stability while maintaining its binding affinity, solving the problem of rapid metabolism without sacrificing effectiveness.  Introducing metabolically susceptible groups Drug activity can be prolonged by inhibiting metabolism, but drugs that are extremely stable and slow to excrete can pose problems. It's desirable for drugs to do their job and stop within a reasonable time to avoid toxicity and side effects. Introducing metabolically susceptible groups Introducing groups that are susceptible to metabolism is a good way of shortening the lifetime of a drug. For example, a methyl group was introduced to the anti- arthritic agent L 787257 to shorten its lifetime. The methyl group of the resulting compound ( L 791456 ) was metabolically oxidized to a polar alcohol, as well as to a carboxylic acid.  Another example is the analgesic Remifentanil, where ester groups were incorporated to make it a short-lasting agent. The beta-blocker Esmolol was also designed to be a short- acting agent by introducing an ester group.  self-destruct drug A self-destruct drug is one that remains chemically stable under certain conditions but becomes unstable and degrades spontaneously under different conditions. The key feature is that the drug inactivates itself without relying on metabolic enzymes, which can vary between patients. The main advantage of self-destruct drugs is that inactivation is independent of the patient’s metabolic enzymes, making the drug’s action more predictable across different individuals.  Example: Atracurium: Atracurium is a neuromuscular blocking agent that is stable at acidic pH but self-destructs when it encounters the slightly alkaline conditions of the blood. This property allows atracurium to have a  Targeting drugs Major goals in drug design is to find ways of targeting drugs to the exact locations in the body where they are most needed. Drugs can be made more selective to distinguish between different targets within the body. 1.Targeting tumour cells: ‘search and destroy’ drugs The major goal in cancer chemotherapy is to target drugs efficiently against tumour cells rather than normal cells.  Attachment of drug to an important ‘building block’ The idea is to attach the active drug to an important ‘building block’ molecule that is needed in large amounts by the rapidly dividing tumour cells. Building block could be Amino acid or a nucleic acid base. Tumour cells often grow more quickly than normal cells and require the building blocks more urgently. Therefore, the uptake is greater in tumour cells.  Attachment of drug to monoclonal Monoclonal antibodies recognize antibodies unique to the antigens tumour cell. Once the antibody binds to the antigen, the drug or poison is released to kill the cell. Difficulties in this approach include 1. Identification of suitable antigens 2. Production of antibodies in significant quantity.  2.Targeting gastrointestinal infections If a drug is to be targeted against an infection of the gastrointestinal tract, it must be prevented from being absorbed into the blood supply. This can be done by using a fully ionized drug that is incapable of crossing cell membranes e.g., highly ionized Sulphonamides.  3.Targeting peripheral regions rather than the central nervous system Increasing the polarity of drugs, less likely to have CNS side effects why? They are less likely to cross the blood– brain barrier. Achieving selectivity for the CNS over the peripheral regions of the body It is not so straightforward To achieve that, the drug would have to be designed to cross the blood–brain barrier efficiently, while being metabolized rapidly to inactive metabolites in the peripheral system.  4.Targeting with membrane tethers One way to targeting cell membrane is to attach membrane tethers to the drug such that the molecule is anchored in the membrane close to the target. Membrane-Tethered Drug Targeting β-Secretase for Alzheimer’s Disease Objective: Inhibit β-secretase to reduce toxic protein aggregates endosomes. Mechanism & Targeting: A peptide-based inhibitor is attached to a sterol, allowing endocytosis to direct the drug specifically to endosomes, where β-secretase is highly active.  Mitochondria-Targeted Agent for Alzheimer’s Disease (AD) Treatment AD leads to the generation of radicals and oxidation reactions that are damaging to the cell. MitoQ contains an antioxidant prodrug linked to a hydrophobic triphenylphosphine moiety. The latter group aids the drug’s entry into mitochondria, then tethers it to the phospholipid bilayers of the mitochondria membrane. The quinone ring system is reduced rapidly to the active quinol form which can then act as an antioxidant to neutralize free radicals.  Reducing toxicity It is often found that a drug fails clinical trials because of toxic side effects. This may be due to toxic metabolites it is also worth checking to see whether there are any functional groups present that are particularly prone to producing toxic metabolites. E.g., aromatic nitro groups, aromatic amines, bromoarenes, hydrazines, hydroxylamines, or polyhalogenated groups. UK 47265 and Fluconazole polyhalogenated group The halogen substituents of the antifungal agent UK 47265 were varied to find a compound that was less toxic to the liver. This led to the successful antifungal agent fluconazole.  Prodrugs Prodrugs are compounds which are inactive in themselves, but which are converted (Usually by a metabolic enzymes)in the body to the active drug. Esterase enzymes, N -demethylation, decarboxylation, and the hydrolysis of amides and phosphates.  Prodrugs to improve membrane permeability Esters as prodrugs Ionizable group (e.g., carboxylic acid) may prevent it from crossing a fatty cell membrane. The less polar ester can cross fatty cell membranes and, once it is in the bloodstream, it is hydrolysed back to the free acid by esterases in Esters as prodrugs  Too reactive ester = Chemically unstable ester Too reactive ester are hydrolysed by the acid/ alkaline conditions GIT. Cyclopropane carboxylic acid esters have been studied as potential prodrugs because the cyclopropane ring could stabilize the carbonyl group of a neighboring ester. A conjugated double bond stabilizes a neighboring carbonyl group due to interaction of the π-systems involved.  improve membrane permeability: N - Methylated prodrugs Polar amines can be N - methylated to: reduce polarity and improve permeability. Several hypnotics and anti- epileptics take advantage of this reaction, e.g., Hexobarbitone. In liver  improve membrane permeability: Trojan horse approach for transport proteins A prodrug is designed to take advantage of transport proteins in the cell membrane. E.g. levodopa: prodrug for the neurotransmitter dopamine.  Dopamine itself cannot be used as it is too polar to cross the blood– brain barrier. Levodopa is even more polar and seems an unlikely prodrug, but it is also an amino acid, and so it is recognized by the transport proteins for amino acids which carry it across the cell membrane.  Prodrugs to prolong drug activity 6-mercaptopurine drug used to suppresses the body’s immune response, and it tends to be eliminated from the body too quickly. The prodrug azathioprine has the advantage that it is slowly converted to 6- mercaptopurine by being attacked by glutathione. The rate of conversion can be altered, depending on the electron- withdrawing ability of the heterocyclic group. The greater the electron-withdrawing power, the faster the breakdown.  Valium and Librium might be prodrugs and activated by N - demethylation to nordazepams. Nordazepam itself has been used as a sedative but loses activity quite quickly because of metabolism and excretion.  Another way to maintain sustained drug levels over time is to attach a highly lipophilic group to the drug which leads to slower drug release from the fat tissue of the body E.g. The antimalarial agent cycloguanil pamoate.  Prodrugs masking drug toxicity and side effects Salicylic acid is a good painkiller but causes gastric bleeding because of the free phenolic group. This is overcome by masking the phenol as an ester ( aspirin ).  Prodrugs masking drug toxicity and side effects Diazepam has a drowsiness side effect due to the high initial plasma levels following administration. LDZ is an example of a diazepam prodrug which avoids this side effect. An aminopeptidase enzyme hydrolyses the prodrug to release a non-toxic lysine moiety, and the resulting amine spontaneously cyclizes to the diazepam. An aminopeptidase enzyme hydrolyses the prodrug to release a non-toxic lysine moiety Prodrugs to lower water solubility One way to avoid revolting taste of drugs is to reduce their water solubility to prevent them dissolving on the tongue. The bitter taste of chloramphenicol can be avoided by using its palmitate ester form, which is more hydrophobic due to a masked alcohol group and a long-chain fatty group. This form doesn’t dissolve easily on the tongue and is quickly hydrolyzed after swallowing.  Prodrugs to improve water solubility 1. Drugs which are given intravenously. succinate ester of chloramphenicol (extra carboxylic acid). 2. To improve the absorption of non-polar drugs from the gut. 3. Preventing the pain associated with some injections. To improve the absorption of non-polar drugs from the gut. Drugs must have some water solubility if they are to be absorbed, otherwise they dissolve in fatty globules and fail to interact effectively with the gut wall e.g., estrone.  Preventing the pain associated with some injections. Pain is caused by the poor solubility of the drug at the site of injection. The antibacterial agent clindamycin is painful when injected, but this is avoided by using a phosphate ester prodrug which has much better solubility because of the ionic phosphate group.  Prodrug used in the targeting of drugs  Methenamine : a prodrug is stable and inactive at pH levels above 5 degrades in acidic conditions to release formaldehyde, an antibacterial agent. This is useful for treating urinary tract infections, as methenamine remains unchanged in the slightly alkaline blood (ph 7.4 )but activates in the acidic environment of infected urine. 57  Proton pump inhibitors are also prodrugs, becoming   Prodrugs to increase chemical stability Ampicillin : an antibacterial agent, is prone to decomposition in concentrated solutions due to an intramolecular reaction on side chain amino group. Hetacillin : a prodrug stabilizes ampicillin by locking its reactive nitrogen in a ring, preventing this reaction. hetacillin gradually releases ampicillin and acetone through esterase. 58   Prodrugs activated by external influence "sleeping agent" is(sleeping agents) a type of prodrug that remains inactive until activated by an external influence. In photodynamic therapy, photosensitizing agents like porphyrins are administered intravenously, accumulating selectively in tumor cells. When the cancer cells are irradiated with light, they convert to an excited state, reacting with oxygen to produce toxic singlet oxygen, which kills the tumor cells. 59   Drug alliances ( Sentry drugs Certain drugs ) the effectiveness or stability of can enhance other drugs through "drug alliances.“ One method is using a "sentry" drug, which protects or assists the primary drug by inhibiting enzymes that would otherwise metabolize it. Example clavulanic acid protects penicillins by inhibiting β-lactamase. In AIDS treatment, combines ritonavir and lopinavir. Ritonavir strong enzyme inhibitor, slows the metabolism of lopinavir, allowing for lower doses to 60 achieve therapeutic levels.  In Parkinson’s disease treatment, levodopa is used as a prodrug for dopamine. large doses cause side effects like nausea due to dopamine buildup in the peripheral blood, as levodopa is converted by the enzyme dopa decarboxylase before reaching the brain. Carbidopa an inhibitor of this enzyme, being highly polar, does not cross the blood- brain barrier, allowing levodopa to convert to dopamine only in the brain. 61  Localizing a drugs area of activity Adrenaline is used to localize the activity of the local anesthetic procaine. When injected together, adrenaline constricts nearby blood vessels, slowing the removal of procaine from the area and prolonging its anesthetic effect. Increasing absorption Metoclopramide is used with analgesics in migraine treatment to increase gastric motility, which speeds up analgesic absorption and provides faster pain 62   Endogenous compounds as drugs Endogenous compounds, naturally occurring in the body, have potential as medicines. Since hormones act as natural messengers, they could be used therapeutically instead of synthetic drugs. Endogenous molecules like neurotransmitters, hormones, peptides, proteins, and antibodies as drugs. 63   Neurotransmitters Non-peptide neurotransmitters, though easily synthesized, are unsuitable as drugs. 1. They are often unstable in the stomach, require injection, and are quickly inactivated and removed by the body. 2. Direct administration can cause side effects. 3. Natural neurotransmitters also act on all receptor subtypes, risking overdose in unintended areas, whereas synthetic drugs can target specific receptor subtypes. 4. Neurotransmitters can lead to tolerance and addiction. Thus, neurotransmitters cannot effectively serve as medicines. 64  Natural hormones, peptides, and proteins as have significant potential drugs drugs since as therapeutic they circulate in the body similarly to pharmaceuticals. For example, adrenaline is widely used to treat severe allergic reactions. Many therapeutic hormones, including insulin and erythropoietin, and their production has been greatly enhanced by genetic engineering techniques. This method allow for producing sufficient quantities of these proteins. 65  Example:  Recombinant enzymes like glucarpidase have been developed to help cancer patients with failed kidneys when they are taking methotrexate. The enzyme metabolize methotrexate and prevent it from reaching toxic levels. Some endogenous peptides and proteins have been ineffective in treatment, often due to their complexity or instability in the body. Another reasons due to their susceptibility to digestive and metabolic enzymes, poor gut absorption, and rapid clearance from the body. 66  PEGylation has been developed, where polyethylene glycol (PEG) is attached to proteins to enhance their solubility, stability, and resistance to immune reactions. This modification increases the protein's size, preventing kidney filtration and prolonging its presence in the bloodstream. PEGylated proteins, such as pegaspargase for leukemia and pegademase for severe combined immunodeficiency (SCID) syndrome, 67   Antibodies as drugs Biotechnology companies are increasingly developing antibodies and antibody-based drugs through genetic engineering and monoclonal antibody technology. Antibodies can specifically recognize cancer cells or viruses, making them valuable for targeted drug delivery. 68  Examples : Omalizumab (approved in 2003): Treats allergic asthma by binding to immunoglobulin E (IgE).Prevents IgE from triggering chemicals responsible for asthma symptoms. Adalimumab (launched in 2003): First fully humanized antibody, used for rheumatoid arthritis. Binds to the inflammatory cytokine TNF-α, preventing receptor interaction and tagging cells for immune destruction. 69   Piptides and piptidomimetics in drug design Endogenous peptides and proteins are crucial lead compounds in the development of new drugs, with examples including renin inhibitors, protease inhibitors, and luteinizing hormone-releasing hormone agonists. Peptides and proteins generally suffer from poor absorption or metabolic susceptibility. 70   Peptidomimetics Modifying the peptide structure to create peptidomimetics, which are more easily absorbed, and more resistant to digestive and metabolic enzymes. To enhance bioavailability, chemically or enzymatically sensitive peptide bonds in a compound can be substituted with more stable functional groups. 71  Examples on modification :  Replace a susceptible peptide bond with a more stable functional group to resist hydrolytic attack by peptidase enzymes. Example: Replace a peptide bond with an alkene, which mimics the double bond nature of peptides and is not broken down by peptidases. 72  Replace an L-amino acid with the D- enantiomer: This change alters the side chain orientation, making the molecule harder for digestive enzymes to recognize. Limitation: The modified molecule may also become less recognizable to the target receptor. 73  Replace natural amino acids with unnatural ones: Used in structure-based drug design to increase binding affinity and reduce enzyme recognition. X-ray crystallography and molecular modeling help identify binding subsites in target proteins. Example: In saquinavir, an L-proline residue was replaced with a decahydroisoquinoline ring 74   Peptide drugs Have challenges in pharmacokinetics that make the use of peptides as drugs often reluctant, but they still play a significant role in medicinal chemistry. 1. Ciclosporin, an orally administered immunosuppressant. 2. Enfuvirtide is the first drug in a new class of anti-HIV treatments; it is a 36-amino-acid polypeptide injected subcutaneously. 3. Teriparatide is peptide drug given by subcutaneous injection to osteoporosis. Overall, peptide drugs can be effective when appropriately chosen for specific diseases and methods 75 of administration.   Oligonucleotides Are being explored as antisense drugs and aptamers, there are disadvantages due to rapid degradation by nucleases and difficult absorbed through cell membrane due to their large size and high charge. Modifications have been made to their phosphate linkages, such as phosphorothioates and methylphosphonates, which show promise as therapeutic agents. 76  Example Oblimersen an antisense drug developed by Genta, consisting of 18 deoxynucleotides linked by a phosphorothioate backbone. It targets the mRNA of the Bcl-2 protein, which inhibits apoptosis, potentially enhancing cancer treatment efficacy when used with chemotherapy drugs like docetaxel and irinotecan. 77 QSAR Chapter 18 Part 1  Strategies in drug design There are different strategies to design a drug including : 1 change in shape ( to make a drug better fit for its target binding site ) 2change in functional groups or substituents to improve the pharmacokinetics such as; absorption,distribution,metabolism,and, and elimination) or binding site interactions of the drug. 3synthesis of analogues containing a range of substituents on aromatic or heteroaromatic rings or accessible functional groups. A fact Its important to mention that the number of possible analogues is infinite if we were to try and synthesize analogues with every substituent and combination of substituents is possible. But, if a rational drug design approach can be followed in deciding which substituents to use this would be advantageous.  What is QSAR approach? It is a rational drug design approach that attempts to identify and quantify the physicochemical properties of a drug and to study them influences see whether any of these properties influences the drug’s biological activity. If there is a relationship between these properties and the biological activity, an equation can be drawn up to quantify the relationship and to allow the medicinal chemist to say with some confidence that the property has an important role in the pharmacokinetics or mechanism of action of the drug.  Any drug have many physicochemical properties (structural physical ,or chemical) so, it would be difficult to quantify them all and relate them all to biological activity at the same time. So, there is a simple and more practical approach to consider one or two physicochemical properties of the drug and to vary them while attempting to keep other properties constant.  A range of compounds is synthesized in order to vary one property and to test how this affects the biological activity then a graph is drawn to plot the biological activity versus the physicochemical feature.  Conditions to apply the QSAR approach 1- the compounds must be structurally related 2- the compounds must act at the same target 3-the compounds must have the same mechanism of action 4-It is also crucial that the correct testing procedures are used Hydrophobicity Studying the hydrophobic character of a drug is crucial because it tells us how easily the drug crosses cell membranes and also it maybe important in receptor interactions. Biological activity versus log p Note: log(1/C) is the biological activity Log P:hydrophobicity  In studies where the range of the log P values is restricted to a small range (e.g. log P = 1–4), a straight-line graph is obtained showing that there is a relationship between hydrophobicity and biological activity.  linear regression analysis by the least squared method It is a procedure to draw the best possible line through the data points in the graph. The best line will be the closest to the data point. The procedure : 1. We will draw vertical line from each point. 2. These verticals are measured and then squared in order to eliminate the negative values. 3. We will calculate the sum of squares. 4. The best line through the points will be the line where this total is minimum.  The equation of the straight line will be : y = k 1x + k 2 where k1 , k2 are constants After that we must see whether the relationship is meaningful. so statistical evidence must be obtained to support the QSAR equation and quantify the goodness of fit. this whole prosses can be done speedily using relevant software.  The partition coefficient (p) Experimentally, the hydrophobic character of a drug can be measured by testing its relative distribution in an n -octanol/water mixture. Hydrophobic molecules. will prefer to dissolve in the n -octanol layer of this two-phase system. The relative distribution is known as partition coefficient (p). P = Concentration of drug in octanol / Concentration of drug in aqueous solution. The substituent hydrophobicity constant (π) a measure of how hydrophobic a substituent is relative to hydrogen. It is obtained by measuring the partition coefficient P for a standard compound, such as benzene, with and without a substituent (X). A positive value indicates the substituent is more hydrophobic than hydrogen, while a negative value indicates it is less hydrophobic.  P versus π The partition coefficient P is a measure of the drug’s overall hydrophobicity. The π factor measures the hydrophobicity of a specific region on the drug's skeleton and if it is present in the QSAR equation. if it is present in the QSAR it could emphasize important hydrophobic. interactions involving that region of the molecule with the binding site. Electronic effects The electronic effects have an effect on the ionization of the drug ( polarity) and this have an effect on how easily a drug can pass through cell membranes or how strongly it can interact with the binding site. The Hammett substituent constant (σ) It’s a measure of the electron-withdrawing or electron-donating ability of a substituent. How is it measured? by measuring the dissociation of a series of substituted benzoic acids compared with the dissociation of benzoic acid itself.  Benzoic acid is a weak acid ,so it is partially in the water as the following equation: KH and Kx KH: the equilibrium or dissociation constant when there is no substituent on the aromatic ring. Kx: the equilibrium or dissociation constant for a specific substituent.  The subscript(H) signifies that there are no substituents on the aromatic ring. What if there is a substituent on the aromatic ring ? 1. If the substituent is an electron-withdrawing group : the aromatic ring will have a stronger electron-withdrawing and stabilizing influence on the carboxylate anion, and so the equilibrium will shift more to the ionized form.(Kx>Kh) 2.If the substituent is an electron-donating group: the aromatic ring will be less able to stabilize the carboxylate anion with a smaller Kx value (Kx