Approaches to lead optimization 新加坡国立大学药物化学课件

Approaches to lead optimization 新加坡国立大学药物化学课件 Approaches to Lead Optimization 2006/2007 Learning Objectives: Optimization of lead structures lies at the heart of medicinal chemistry. In this topic, the approaches to optimizing lead structures are discussed, with the purpose of imparting, wherever possible, the reasons why these changes are made. Examples of how these approaches are applied to drug design are discussed. References: 1. Silverman RB: Chapter 2. 2. Foye’s Principle of Medicinal Chemistry Chapter 2. 1 A lead structure is defined as a compound that has shown acceptable levels of activity and selectivity in a pharmacological or biochemically relevant assay. However, there is always a need to improve on the lead structure so that it can fulfill the requirements for clinical usefulness. Thus the lead compound must be modified and these activities are collectively referred to as “lead optimization or lead modification”. Lead optimization may be seen as a means of defining that part of the molecule that is involved in interacting with the biological target (enzyme or receptor). Drugs act by binding specifically to biomacromolecules. A specific and unique 3D structure of the drug molecule is a prerequisite for activity. The initial step in the formation of a drug-receptor complex is a recognition event. The receptor has to recognize whether an approaching molecule possesses the requisite features necessary for binding. These requisite features are broadly referred to as the pharmacophore. Pharmacophore : ensemble of steric and electronic features that is necessary to ensure the optimal interactions with a specific biological target structure and to trigger /block its biological response. It is an abstract concept that accounts for the common molecular interaction capacities of a group of compounds towards their target structure. The pharmacophore can be considered as the largest common denominator shared by a set of active molecules. The 3D structure of many receptors and enzymes remain unknown. Knowledge of the pharmacophore of a class of drugs (even if it is hypothetical) is an important source for understanding drug-receptor interactions at the molecular level. In order to describe the pharmacophore pattern correctly, the steric and electronic features of the bioactive conformation of the drug molecules have to be determined. The availability of a set of compounds from a distinct class of candidates showing a large variety of chemical structure and which interact via the same binding mechanism with the same receptor is an ideal starting point for the identification of a pharmacophore. If the medicinal chemist is uncertain about the structural features of the pharmacophore, an initial goal of lead modification would be to define the pharmacophore – that is to determine what changes can be made that will retain or reinforce activity, and what changes will lead to loss of activity. This approach is called pharmacophore (or analog) based drug design. In analog design, modification of the lead compound can involve one or more of the following strategies: 2 , Bioisosteric replacement , Conformational restraint , Functional Group Modification 1. Bioisosteric Replacement A bioisostere is a compound resulting from the exchange of an atom or of a group of atoms with another, broadly similar, atom or group of atoms. Bioisosteres are groups or substituents that have chemical or physical similarities, and which produce broadly similar biological properties. The objective of a bioisosteric replacement is to create a new compound which interact with same target protein as the parent compound. The bioisosteric replacement may be physicochemically or topologically based. Bioisosterism is an important lead modification approach that has been shown to be useful to attenuate toxicity, modify activity of the lead, alter PK properties or to circumvent previous patent coverage of leads in the literature. (a) Classical and Non-classical Bioisosteres Classical bioisosteres are basically isosteres : molecules or ions with the same size, having the same number of atoms or valence electrons. Classical bioisosteres include: (i) Monovalent atoms and groups - F, H - OH, NH - SH, OH -Cl, Br, CF 3 (ii) Bivalent atoms and groups - CH, NH, -O- 2 - -COCHR, CONHR, COOR, COSR 2 (iii) Trivalent atoms - -CH= and –N= (iv) Ring equivalents - -CH=CH- and –S- (benzene and thiophen) Pseudoatoms are also isosteres: 3 Grimm’s hydride displacement law states that the addition of H to an atom confers on the aggregate the properties of the atom of the next highest atomic number. - - For example: Fand OHare pseudoatoms and should share similar physical properties (ie are isosteres) 2-+-H is added intranuclearly (into nucleus): O + H , F 2-+-H is added to peripheral electron shell : O + H , OH Non Classical Bioisosteres They are replacements of functional groups not defined by classical definitions. Some sources prefer to describe bioisosteres as “non-classical isosteres” and reserve the term isosteres for classical examples. Examples of bioisosteres in drug design are given in the following paragraphs. (b) Carboxylic acid and tetrazole Losartan is an angiotensin II (Ang II) receptor antagonist. Inhibition of the Ang II receptor will limit the pressor, antinatriuretic and hypertropic effects of Ang II and thus lead to a reduction of blood pressure. stThe lead compound was EXP 7711, which was the 1 of several analogues to show oral activity. However, EXP 7711 has a poor PK profile. Cl ClN NCHOHHnC249NCHOHnCH249N N HNHOOCNNEXP 7711Losartan 0.23 uMICIC 0.019 uM5050ED (p.o) 11 mg/kgED (p.o) 0.59 mg/kg5050 4 * Compare the carboxylic acid and the tetrazole ring in terms of acidity, size and lipophilicity. NN O N HNHO carboxylic acidTetrazole Tetrazole as an acid : NNNNNNNN NNNNNNNN Tetrazole is an NH acid. Normally NH acids are weaker than OH acids (carboxylic acid). But in this case, tetrazole is comparable to carboxylic acid in terms of acidity (pKa of tetrazole = 4.8). (c ) Hydrogen and Fluorine X = H X = F X = Cl X = CF X = CH 33 Bond strength 93 114 72 - - C-X (kcal /mol) VDW radius of X 1.20 1.35 1.80 - - (A) , of X 0.00 0.14 0.71 0.88 0.56 Molar refractivity 0.103 0.92 6.03 5.02 5.65 , of X (para, 0.00 0.06 0.23 0.54 -0.17 aromatic) ,* of X (aliphatic - 3.08 2.68 2.85 0 system) Mesomeric Effect 0 -0.34 -0.15 0.19 -0.13 (R, aromatic system) Molar refractivity is the molar volume corrected by the refractive index. It represents size and polarizability of a fragment or molecule. - F is considerably smaller than the rest of the halogen atoms. 5 - C-F bonds are particularly stable. F- is a poor leaving group and thus C-F is rarely ionized or displaced. This explains why F derivatives are more resistant to metabolic degradation. - The electronegativity of F exceeds that of the other halogens. ,* = inductive effect in aliphatic system. F has a value of +3.08 (strongly electron withdrawing). - F has lone pair of electrons and these electrons can be delocalized when F is attached to a benzene ring or to C=C. Thus, F has a negative R value (ie it is electron donating by mesomeric effect, +M). - The , (para) value of F combines the opposing inductive aromatic (withdrawing) and mesomeric (donating) effects. The net effect is a relatively small electron withdrawing effect, indicating that the two effects are quite balanced. - Another difference between F and other halogens comes from the absence of d orbitals for F and thus, its inability to participate in resonance effects with a donor of , electrons. +XOHOHX Resonance between OH lone pair and X is not possible when X = F This explains why p-fluorophenol is less acidic than phenol. On the other hand, chloro-, bromo and iodophenols are more acidic than phenol. Compound pKa Phenol 10.49 p-F phenol 10.58 p-Cl phenol 9.88 p-Br phenol 9.81 p-I phenol 9.66 A good example of a bioisosteric replacement involving F and H is seen in 5-fluorouracil. 6 O RR = H : Uracil HNR = F 5-fluorouracil ONH 5-Fluorouracil (5FU) is an anticancer drug. Its mode of action is based on its ability to “mimic” uracil. Uracil (in the form of the nucleoside 2’-deoxyuridylic acid or dUMP) is converted to 2’deoxythymidylic acid by the enzyme thymidine synthetase (cofactor = folate). Thymidylate is an important methyl donor and is one of the critical bases for DNA synthesis. 5FU is converted to 5-fluoro-2-deoxyuridylic acid (FdUMP), which readily binds to thymidine synthetase and the folate cofactor. Folate would normally transfer 2 H atoms and a methylene group to uracil to form thymidine. This reaction cannot take place in 5-F-uracil because of the stability of the fluorine-carbon bond in F-dUMP. Result: sustained inhibition of the enzyme thymidylate synthetase by FdUMP. (d) Phenol and indole / N containing heterocycles The most popular surrogate for phenolic functions are NH groups rendered acidic through the presence an electron attracting group. This is seen in the following examples: 7 OH N NN NNNHHHIndoleIndazolebenzotriazole HN OO NNHH indolonebenzoimidazolone HON OS NNHH benzoimidazole-thionebenzoxazolone The N containing heterocycles retain the H bond donating property of the phenolic OH. The more acidic the NH, the more available is the H for H bonding. Acidity of NH is enhanced by placing the N in a 5 membered aromatic ring, and by locating electron withdrawing groups in the vicinity of the NH group. But there are important differences between phenol and these bioisosteres: - size differences - metabolic susceptibility (phenol > N heterocycles) (e) Sulphur and an ethylenic group (C=C) This is a good example of classical isosteres. The S atom is approximately equivalent to the ethylenic group in terms of size (MW of –CH=CH- is 26, atomic mass of S is 32) and ability to provide delocalizable electrons. Benzene and thiophene are widely considered to be ring equivalents. 8 - Both are aromatic compounds with 6 , electrons. - Molecular weights in the same range oo- Have similar boiling points (80 for benzene, 84 thiopene) Similarity in boiling points is often used to identify isosteric ring systems. When boiling points are similar, other physicochemical properties are likely to be the same – for example, solubility, dipole moments. S ThiopheneBenzene 2. Conformational restriction 9 (i) Theoretical Considerations In biology, noncovalent interactions are of primary importance and many issues in medicinal chemistry hinge on understanding the bimolecular noncovalent interactions using a receptor and ligand /drug. At equilibrium, the interaction of a ligand / drug with its receptor can be described in terms of its association constant Ka or dissociation constant Kd. Ka = 1/Kd Ka Kd kk1-1Equation DRDRD + RD + Rkk-1 1 Definition k / k k / k 1 -1-1 1 Strong affinity Large Ka (DR forms Small Kd (DR does not between D and R readily) dissociate readily) given by: -1Unit M M Both Ka and Kd are experimentally accessible by direct measurement of the energy of the interaction, using the Gibbs-van’t Hoff relation: Log K = - , G / RT where ,G = ,H –T ,S K can be Ka or Kd. As a general consideration, if , G is negative, it means that the chemical process is spontaneous. DRD + R(i) For Negative , G means forward reaction is spontaneous, and favours formation of DR. DRD + R(ii) For Negative , G also means forward reaction is spontaneous which does not favour drug-receptor interaction. Therefore when using Kd to describe DR interaction, + ,G indicates a “favourable” interaction. ,G is determined by ,H (enthalpy) and ,S (entropy) ,G = ,H –T ,S (ii) Enthalpy and entropy changes in DR interaction 10 Enthalpy considerations Enthalpy (,H) is a measure of the heat content of a substance. Entropy S is a measure of the unusable energy or disorder in a system. When the drug interacts by forming covalent bonds with the receptor (irreversible), the contribution to ,G is usually dominated by ,H. If the more usual non-covalent bond is formed, then the contributions by ,H and ,S are often comparable. Bond formation releases energy and is accompanied by a loss in enthalpy (= - ,H) Bond breaking requires energy input and causes a gain in enthalpy ( = + ,H) Entropy considerations Before the interaction, the drug and the receptor have translational and rotational flexibility. These are entropy rich movements. Once the association occurs, these degrees of motion are lost. If ligand is flexible, it has many rotatable bonds. These rotatable bonds are frozen when the ligand associates with its receptor. This results in a loss of rotational (torsional) entropy which is approximately equal to 0.7 kcal /mol for the freezing up of one rotatable bond. These entropy penalties will render ,S negative. Accordingly, the free energy change for association (,G) becomes smaller (a smaller negative number). In order to retain an association constant of a reasonable value, a flexible ligand has to compensate the loss in entropy by a greater loss in enthalpy. That is the loss in entropy must be offset by more favourable intermolecular interactions, such as H bonds, van der Waals packing, and coloumbic interactions, all of which will contribute to a larger (and favourable) enthalpy loss (a more negative ,H). Mention must be made of the gain in entropy accompanying DR interaction. This gain is associated with the desolvation of functional groups and the occurrence of hydrophobic forces. 11 Figure 1 D and R Before interaction DR Complex Figure 1 shows a trifunctional drug and its receptor. Small circles = water molecules. Functional groups on receptor and drug are hydrated. When interaction occurs between drug and receptor, these water molecules must be removed. This is called desolvation and involves bond breaking and input of energy (+,H). The free drug has an overall rotational and translational entropy (,Srt) and an internal entropy. On binding, both entropy functions are lost but the loss in entropy is compensated by the increase in entropy due to loss of structured water on binding, as well as an increase in entropy due to low frequency vibrational modes associated with DR noncovalent bonds (indicated by ---- in Figure). While ,Srt is independent of size, the other entropic and enthalpic terms depend on the number and nature of functional groups present. Of particular importance is the increase in entropy when water molecules are freed when nonpolar surfaces interact with each other. It is this increase in entropy which drives the association of nonpolar groups, which is normally described as hydrophobic interactions. It is important because most entropic changes involved in the drug-receptor interaction result in a loss (not gain) in entropy. Therefore a common strategy in drug design is to increase the nonpolar portions in the ligand as this will increase entropy. (iii) Examples of Conformational restricted analogues The advantage of conformational restriction is that a smaller loss in entropy is encountered on binding. This is because rotatable bonds are already frozen in the rigid analogue / locked conformation. Hence there is little or no loss in torsional entropy when drug/ligand and receptor interacts. This is the free energy advantage enjoyed by conformationally restricted ligands compared to flexible ligands. Conformationally restricted analogues of capsaicin: One of the most recent pain targets has been modulated unknowingly for centuries. It is linked to the natural product capsaicin, the pungent 12 component of chilli peppers. Folk medicine mentions the use of hot pepper extracts to relieve tooth ache and chilli pods have been massaged on inflamed gums to relieve dental pain. The active substance in the chilli pepper is capsaicin. It is the active substance of several analgesic creams to relieve minor aches and pains of muscles and joints. O COH3NH HO Capsaicin The mechanism by which capsaicin brings about analgesia is not well understood. One school of thought proposes that capsaicin stimulates a certain population of sensory neurons until they become insensitive to further stimulation. Capsaicin reduces levels of substance P (a neurotransmitter) associated with pain. What is more interesting is that the analgesia of capsaicin is preceded by an intense and painful hyperalgesia caused by activation of a non-selective cation channel known as the vanilloid receptor 1. In other words, capsaicin stimulates this receptor. The vanilloid receptor has gained considerable interest as a target for pain relief. What is required is an agent that would block the activation of this receptor. Since capsaicin interacts with the receptor, it has been used as a lead structure for developing antagonists. One class of compounds that have emerged from lead modification of capsaicin is a group of N-arylcinnamides. A conformational analysis was carried out to gain an understanding of the preferred orientation of the enone moiety. It was found that the s-cis conformation is preferred to the s-trans by about 2.6 kcal/mol (see example with a representative compound). )C(CH33 O)C(CH33 HONHON OOO s-ciss-trans Therefore, it was proposed that the s-cis conformation is the bioactive conformation. To test this hypothesis, the s-cis conformer was restricted in the following ways: A: By connecting the amide N to the , position of the cinnamide to form the lactam 13 B: By incorporating the β position of the cinnamide and amide carbonyl into various 6 membered aromatic rings. A )C(CH33 HON OOB )C(CH33)C(CH33OVZON WYOOXO )C(CH33 ON OO Some variations of the structure obtained from step B are shown below: )C(CH33)C(CH33 HHONON NOON )C(CH33)C(CH33HONHON NNNOON )C(CH33 OX NNO X=N(CH3),S,O,CH2 Example of entropy-enthalpy compensation among ,-adrenergic agonists and antagonists 14 Agonist (-) isoproterenol -9.3 -13.3 -12.9 6.6 (-) norephedrine -7.9 -18.8 -35.3 5.6 Antagonist (-) propanolol -12.5 -3.8 +27.9 8.8 Pindolol -11.8 -5.0 +21.8 8.4 Atenolol -7.4 -3.4 +13.0 5.3 Practolol -7.4 +3.9 +36.7 5.2 Sotalol -8.2 -2.1 +19.5 5.8 Agonists and antagonists have very similar binding energies but different entropies and enthalpies of binding. These differences have important implications. These will be discussed in the lecture. Conformation restriction of acetycholine OCH3 1H2+6NCC235CHCHCO33H24CH3 Acetylcholine is an important neurotransmitter. It is a flexible molecule because of rotation about the , bonds. Because of the relatively unrestricted rotation about these bonds, ACH can exist in a number of conformations. Most of the studies on the conformational isomerism of ACH have focused on the torsion angles between the ester O (ether O, marked 4 in figure) and the quaternary N. This is equivalent to the rotation about the C2-C3 bond. Four of these conformations are shown by Newman projections in the following figure: 15 +N+NOCOCH3 OCOCH3 AntiperiplanarSynperiplanar (anti, transoid)(eclipsed, ciscoid) ++NN OCOCH3 OCOCH3 SynclinalAnticlinal (gauche or skew)(gauche or skew) Meaning of syn versus anti, and periplanar vs clinal +30-30PSYN CC ANTIP+150-150 Techniques were used to determine the thermodynamically preferred conformation of ACH. These were NMR (aqueous solution), X-ray crystallography (solid state) and molecular orbital calculations. All 3 methods indicated that ACH assumed a synclinal conformational relationship between the ester oxygen and the quaternary N. Theoretically, one would expect the antiperiplanar conformation to predominate because in this conformation, there will be minimum non-bonded interactions. However, experimental findings point to the synclinal conformer as the preferred conformation. It should be emphasized that the experimentally determined synclinal conformation was determined from the solution and solid states. It may not be the bioactive conformation. 16 Not withstanding the apparent importance of the synclinal conformation, medicinal chemists have synthesized and tested conformationally restricted analogs of ACH in which the two critical groups are trans or cis to each other. One example is the cis and trans isomers of a conformationally rigid analog of ACH : 2-acetoxycyclopropyl-1-trimethylammonium iodide (ACTM). These compounds have a rigid cyclopropyl ring. Thus, the ammonium and acetoxy functions cannot change their relative bond positions by rotation. The cis and trans isomers are rigidly constrained to the conformations shown. o The torsion angle subtended by the two groups is approximately 140 in the otrans isomer and 1 in the cis isomer. Therefore the trans isomer is equivalent to the anticlinal form and the cis is equivalent to the synperiplanar form. OCOCH+(HC)N3H+(HC)N3333 HHHOCOCH3 cis ACTMtrans ACTM When evaluated for muscarinic activity, the trans isomer was found to be a better agonist than the cis isomer. In addition, the trans isomer has two non-superimposable mirror image stereoisomers (ie enantiomers). The (+) trans enantiomer had more activity than the (-) trans enantiomer. The racemic cis compound had almost no activity. (iv) Conformationally restricted compounds and bioavailability An interesting correlation is proposed between the bioavailability of a compound and the number of rotatable bonds present. These studies were carried out using over 1100 drug candidates studied at GSK. Bioavailability was assessed in rats. It was found that reduced molecular flexibility (as measured by number of rotatable bonds*) and small polar surface area (measured by total H bond count = sum of donors and acceptors) were important predictors of good oral bioavailability. This relationship was not dependent on the molecular weight of the compound. 17 Fraction of compounds with a rat oral bioavailability of 20% or greater as a function of MW and rotatable bond count (nrot) Therefore, according to this study, compounds need to comply with only 2 criteria to have good oral bioavailability in rats. They are (i) 10 or fewer 2 rotatable bonds and (ii) polar SA < 140 A(or 12 or fewer H bond donors and acceptors). How does fewer rotatable bonds translate to improved bioavailability ? This finding is significant because until this report, there was a MW limit (500) imposed for a drug to have good bioavailability. What this finding showed was that by freezing some of the rotatable bonds, the MW is no longer an essential parameter to be considered. * Definition of rotatable bond: any single bond, not in a ring, attached to a non-terminal heavy atom (ie any atom except H). 18 3. Substituent Effects The replacement of H in an active molecule by a substituent group can bring about several changes in physicochemical and pharmacological properties : modify potency, duration of action, nature of pharmacological effect. This is because the newly introduced substituent changes solubility, electronic density, steric factors, and has a different capacity to establish interactions with the receptor. (i) Craig Plot A convenient means of characterizing the physicochemical properties (lipophilicity and electronic character) of substituents is given by the Craig Plot. This plot illustrates the utility of using a simple graphical plot of , versus , (aromatic, for para substituent) to guide the choice of a substituent. The activity and potency of a molecule is related to the interactions of the functional groups in the pharmacophore with related groups on the receptor. (ii) Pharmacophore point Filter This is a set of simple rules meant to classify molecular structures as drug-like or non-druglike. Four functional motifs are defined to be important in drug like molecules: sulphonyl amino hydroxyl carbonyl 19 The occurrence of these functional motifs guarantees H bonding capabilities that are essential for specific drug interactions with its targets. These groups can be combined to give “pharmacophore points”. These pharmacophore points include the following functional groups: Amine, amide, alcohol, ketone, sulfone, sulphonamide, carboxylic acid, carbamate, guanidine, amidine, urea, ester. Elaboration on pharmacophore points: - Pharmacophore points are fused and counted as one when their heteroatoms are not separated by more than one carbon atom. - Primary, secondary and tertiary amines are pharmacophore points but not pyrrole, indole, thiazole, isoxazole, other azoles or diazines. - No more than one COOH should be present. - Compounds must have ring structures. - Intracyclic amines that occur in the same ring are fused and counted as one pharmacophore point. For example, piperazine is a pharmacophore point. - Since the purpose is to capture pharmacophore points that potentially provide key interactions with the target proteins, the following groups are excluded: Nitro, imine, nitrile, pyridine The whole idea is based on the observation that nondrug molecules are often underfunctionalized. Therefore, a molecule with less than 2 pharmacophore points fails the filter. If it has more than 7 pharmacophore points, it also fails due to overfunctionalization. 20 ACD: Available Chemicals Directory (General chemical database) CMC: Comprehensive medicinal Chemistry (drug database) MDDR: MACCS-II Drug Data Report (drug database). Examples of compounds that fail: 21 Examples of drugs : Are they druglike when evaluated by pharmacophore point filter ? NOHO2 SOH NHN HNNOHOH HSOOHNO2HO amoxicillin cephalexin O HNOHNNNH2N-OOONHNH metformin AtorvastatinF Pharmacophore filters 1 and 2 (PF1, PF2) After developing PF1 It was then noted that may small CNS active drugs have only one pharmacophore point, and therefore, failed the filter test for drug-likeness. This resulted in a refinement of PF1 to give PF2. PF2 allows compounds with only 1 pharmacophore point to pass, provided the pharmacophore point is a carboxylic acid, amine, guanidine or amidine. (iii) Functional Groups In the following sections, selected functional groups that are commonly encountered in drug molecules are discussed. These are the alkyl groups (methyl will be mentioned in greater detail than other alkyl groups), halogens, hydroxyl OH, carboxylic acid and basic functionalities. 22 (a) Alkyl Groups: Group , , para Molar Refractivity -CH 0.56 -0.17 0.565 3 -CH 1.02 -0.15 1.030 25 - nCH 1.55 -0.13 1.496 37 -cyclopropyl 1.14 -0.21 1.353 -nCH 2.13 -0.16 1.969 49 -sec CH 2.04 -0.12 1.959 49 -t CH 1.98 -0.20 1.962 49 Increasing the number of carbon atoms is called homologation (methyl, ethyl, propyl are homologues). Homologous series: group of compounds that differ by a constant unit, generally CH2 group. Homologation causes an increase in , (more lipophilic) and size (molar refractivity). For many series of compounds, lengthening of a saturated carbon side chain from one (CH3) to five to nine produces an increase in biological activity. But a further lengthening results in a decrease in potency. This phenomenon corresponds to an increase in lipophilicity which permits penetration into cell membranes until water solubility is reduced to a point where it becomes a problem in transport. Comparison of n-propyl and cyclopropyl shows the effect of cyclization: smaller size (MR) and less lipophilic. Mention must be made about the bonding in cyclopropyl: Morescharacter H H H H H Morepcharacter Therefore the C-C bonds in cyclopropane are “bent” and are intermediate in character between , and ,. This gives them some resemblance to the double bond in unsaturated compounds. 23 The electron donating capacity (, para) of cyclopropyl is greater than n- propyl. No conclusive reason for this increase. It may be that the bond linking cyclopropyl to the aromatic ring is now shorter (more s character). Since the inductive effect is distance dependent (decreases with increasing distance), the shortened distance may contribute to a greater electron donating effect. The normal, secondary and tertiary butyl groups provide insight on the effect of branching on ,, , and size properties. CH3CH3 CH2CHCCH3HCCH22HCCH23 CH3CH3 sec-butylt-butyln--butyl There is a decrease in , values as one goes from n-butyl to t-butyl. t-Butyl has a smaller surface area than n-butyl. One consequence of this reduction in surface area is better solubility in water (more hydrophilic) and this is reflected in the reduction of the , value. The , para of t-butyl suggests it is more electron donating than n-butyl and sec-butyl. Again, there is no good explanation for this observation. The MR of the butyl substituents do not correctly reflect an important property of t-butyl, namely that it is a very bulky group. This is reflected by other steric measures like the Taft steric parameter E. Methyl group Medicinal chemists often refer to the “magic methyl” and how much it can do. A single methyl can disrupt crystal lattices, break hydration spheres, modulate metabolism, enhance chemical stability and displace water as a binding site. Electronic effects of the methyl group 24 The methyl group (and alkyl groups as seen earlier) is the only known functional group that is electron donating by an inductive effect. It also has 2an electron donating hyperconjugative effect when attached to sp hybridized carbon, like an aromatic ring. Effects on solubility The methyl group as a negative , value. Therefore it is a “lipophilic” group and one would expect the introduction of a methyl group to reduce the water solubility of the compound. CH (CH) OH : 8.2 g /100 g HO 3232 CH (CH) OH : 2.4 g /100 g HO 3242 However, there are exceptions. When introduction of the methyl group causes branching in the molecule, solubility actually improves. Reasons are : (i) Reduction in surface area (ii) Reduction in the “packing” of molecules within the crystal lattice by hindering intermolecular interactions. Effects on conformation The methyl group can impose constraints on the rotation of bonds and cause certain conformations to be preferred over others. HParaortho CH HOCH3NOCH3NCH3CH3 Diphenhydramine In diphenhydramine, a para-methyl enhances anti-histamine activity but an ortho-methyl abolishes activity. It is proposed that this is due to restricted rotation about the bond marked with the arrow. The ortho methyl may “clash” with the side chain ether oxygen and this prevent the 2 rings from assuming a coplanar conformation. Effects on metabolism The methyl group is readily oxidized to an inactive (usually) carboxylic acid. The grafting of a methyl group, especially on aromatic rings, is described as a “magnet for metabolizing enzymes”. Can expect a short half-life if a methyl group is present. 25 Example :Midazolam and estazolam: Midazolam is rapidly inactivated (t1.9 h) and is used for anaesthetic 1/2 premedication. Estazolam has a long tof 10-24 h and is used as a sedative-hypnotic. 1/2 The methyl group in midazolam is readily oxidized to an acid which is converted to a water soluble glucuronide and rapidly lost from the body. Estazolam is hydroxylated at position 3 (metabolite is still active) and then converted to glucuronide. The rate of 3-hydroxylation is much slower than ,-hydroxylation of the methyl group. CH3NN NNN 3 NNClCl F Midazolam Estazolam When the methyl group predisposes a compound to metabolism, it may be necessary to replace it with other groups that are resistant to metabolism but have the same size /lipophilicity features as the methyl. Common replacements are chlorine or trifluromethyl: Mainly because of similarity in size to methyl. CH3 -0.17 0.56 5.65 Cl 0.23 0.71 6.03 CF3 0.54 0.88 5.02 26 Tutorial Question: Pls be prepared. R1 N SONH2 N R2HN 2 R1 R2 Solubility Melting pKa % Ionized o at pH 5.2 point (C) (acidic) at pH 5.2 (M) H H 0.0005 252 6.5 4.8 CH3 H 0.0013 234 7.1 1.2 CH3 CH3 0.0024 200 7.4 0.6 The compounds in the table are sulphonamides. (i) An acidic pKa is given in the table. Which group does it belong to ? (ii) Are there other ionizable groups in the sulphonamide ? (iii) Show how the values given in the column “% Ionized at pH 5.2” are derived. (iv) The pKa values in the table shows that the methyl groups reduce the acidity of the sulphonamide. Draw the conjugate base of the sulphonamide with 2 CHgroups. Show the delocalization of the negative charge in this 3 species. Does it explain the acid-weakening effect of the methyl groups ? b. Halogens Currently, 1 out of 3 drugs has one or more halogen atoms. The most common halogen atoms in drugs are chlorine and fluorine. Bromine is less used in drug design because it is reactive and thus, a potentially toxic group. It can generate alkylating reactive intermediates (more so than Cl and F). Care must be exercised when I is introduced into drugs because the C-I bond is weak and I- has good leaving properties. Iodide is also a physiological element. The halogens have been discussed earlier. The following table summarizes the more important properties. 27 C-X Bond strength 114 72 59 45 - (kcal /mol) , 0.14 0.71 0.86 1.12 0.88 Molar 0.92 6.03 8.88 13.94 5.02 Refractivity , para 0.06 0.23 0.23 0.18 0.54 -0.34 -0.15 -0.17 0.19 Resonance Effect c. Hydroxyl OH The substitution of OH for H affects biological activity profoundly, as can be seen from the conversion of ethane to ethanol, or benzene to phenol. i) It is a polar group ( , = -0.67) and will enhance the hydrophilic character of the compound. ii) The phenolic OH is a weak acid (pKa 9.9). On the other hand, the alcoholic OH is a very poor acid (pKa > 15) iii) It is also a source of H bonding. OH can function as a H bond donor (via H) and a H bond acceptor (via lone pairs). Factors that increase the acidity of the OH group will increase the H bond donating ability of the group iv) OH is readily metabolized in phase II conjugation reactions. As a rule, metabolic hydroxylation of an active compound represents a detoxification mechanism. OH groups readily accept activated groups through the action of group transferring enzymes : sulfation, glucuronidation, methylation, phosphorylation). Therefore, presence of an OH group may imply a short ? life for the compound. Common pitfalls in identifying H bond acceptor groups: (i) Already discussed: 28 These are available as H bond acceptors. OTwo lone pairs O Lone pairs on single bonded O are not available as H bond acceptors. (ii) Will be discussed: OO AB O C (iii) N N OO oxazole isoxazole Only lone pairs on =N- are available as H bond acceptors. Lone pairs on Oxygen are delocalized into the ring for aromatic character. d. Carboxylic acids Carboxylic acids are the most common acid functionality in drug molecules. pKa of carboxylic acids range from 4-5 (moderately strong acids). Therefore at physiological pH, the ionized carboxylate form which is more water soluble than the unionized acid, predominates. Therefore the introduction of an acid moiety is widely used as a means of increasing water solubility. The COOH group is electron withdrawing (,para 0.37). Example: Antimalarial agents derived from artemisinin have poor aqueous solubilities. There is an urgent need for a water soluble and injectable form of these drugs to treat severe cases of malaria. The problem was partially solved with the hemisuccinate ester of dihydroartemisinin. This compound 29 (artesunic acid) is given as its water soluble sodium salt (sodium artesunate). But the utility of this compound is undermined by its poor stability due to the facile hydrolysis of the ester linkage. To overcome this problem, a series of analogues in which the solubilizing moiety is joined to dihydroartemisinin by an ether rather than an ester function were prepared. One of the compounds, artelinic acid, is both soluble and stable in alkaline solution, and possesses superior in vivo activity against Plasmodia. CHCH33HHCH3CH3HOOHCHCH33HHOOOCHO3OOHCH3OHOHHOOOHOHHHOCHHCH33OHOOOCH3CHH3OHODihydroartemisininArtemisinin COOH Artelinic acidArtesunic acidCOOH The hemisuccinate present in artesunic acid is described as a half ester. Hemisuccinates of phenols and alcohols may have poor stabilities. Because of the polar characteristics of the carboxylate ion, COOH groups are usually converted to more lipid soluble esters to facilitate passage across membranes. These esters, if inactive, are known as prodrugs. The COOH group is readily metabolized by phase II conjugation : another reason why it may be necessary to protect them as prodrug esters. e. Basic groups The most common basic groups encountered in medicinal chemistry are the amines, amidines, guanidines, and nitrogen containing heterocycles. Review basicities of these groups: Guanidines: pKa 13.6 H NN2+2H+ NNNN1313 30 H22H2HNNN+ + NNNNNN331311 What if protonation occurs at N3 ? 2NN2H+ + NNNN1313H Amidines are structurally similar to guanidines. Also strong bases, protonation occurs on the azomethine nitrogen. (pKa 12.4) H1NN1H+ NN22 Quarternization of amines: Abolish basicity because of loss of lone pair. Compare with protonation of amines CH3+NN Nitrogen containing heteroaromatic compounds NOSN N NNNNNNNHHHHH Pyridine Pyrrole Imidazole Oxazole ThiazolePyrazolePyrimidine Pyridine : pKa 5.4. Protonation at azomethine N. Lone pair is NOT delocalized for 2aromaticity but is situated in an sp hybrid orbital. 31 Addition of another nitrogen into the ring (eg: pyrimidine) reduces basicity further, because the nitrogen introduced into the ring is another azomethine N and is electron withdrawing. Five membered heteroaromatic compounds with nitrogen are , excessive ring systems. Lone pair on N (in pyrrole) is delocalized into the ring for aromatic character and is unavailable for protonation. This property applies to oxazole and thiazole as well. Imidazole is a strong base (pKa 7.4) because it has an azomethine N atom with an available lone pair. Conjugate acid is stabilized by delocalization. 33+NHNH NN+11HH On the other hand, when 2 nitrogen atoms are adjacent to one another (pyrazole), a sharp drop in the basicity of the azomethine N is observed. Cyclic bases have pKa values that are similar to their aliphatic counterparts. HN NNHH piperidine piperazine Basic groups and volume of distribution (Vd) Volume of distribution : measure of the apparent space in the body available to contain the drug. It is the fluid volume required to contain all of the drug in the body at the same concentration as in blood or plasma or water Volume of distribution = [amount of drug in body] / [Concentration] blood/plasma Vd can vastly exceed any physical volume in the body because it is the volume apparently necessary to contain the amount of drug homogenously at the concentration found in the blood, plasma or water. Vd determines half life (t1/2) of a drug. The larger the Vd, the longer the t1/2 of the drug. 32 Half life is the time required to change the amount of drug in the body by one-half during elimination (or during a constant infusion). t = 0.693 Vd / CL 1/2 CL = clearance, Vd = volume of distribution Clearance : measure of the ability of body to eliminate the drug. The introduction of basic groups is associated with an increase in the volume of distribution of the compound. Example: Compound Vd (L/Kg) Clearance ? life (h) (ml/min/ kg) Rifamycin 1.2 80 0.33 Rifampicin 8.8 32 3.5 Rifabutin 266 80 45 33 Compound Log D 7.4 Vd (L/Kg) Clearance ? life (h) (ml/min/kg) Amlopidine 1.8 21.4 7.0 33.8 Felodipine 4.8 9.7 11.8 10.2 Nifendipine 3.2 1.0 8.4 1.9 Nitrendipine 4.2 3.8 21 4.0 Note that rifampicin and rifabutin (ansamycin) have basic side chains (unlike rifamycin). Have much larger Vd and longer half lives. Rifabutin : Vd is too high – suggest that the drug goes into fat/muscle. The following compounds are calcium channel blockers. Note that amlopidine has the largest Vd and the longest t1/2. The log D at pH 7.4 of amlopidine is also the smallest – ie it is more hydrophilic than the other compounds. 34