1. Lecture 3 Organic Pharmaceutical Chemistry Y3 Acid-Base properties of Drugs QSAR

2. Acid-Base Properties of Drugs
Most drugs used today are classified as acids or bases. Acid-base properties of a drug can greatly influence its biodistribution and partitioning characteristics. The definition of Bronsted - Lowry is widely used in pharmacy. An acid is a proton donor and a base is defined as a proton acceptor.
Acid + base ═ Conjugate acid + Conjugate base

3. Acid Strength determines how one predicts in which direction an acid-base reaction lies and to what extent the reaction goes to completion. The pKa contains the information to answer these questions.
Hinderson- Hasselbalch equation can be used to calculate the pH of weak acids, weak bases and buffers consisting of weak acids and their conjugate bases.

4. Examples of acid- base dissociation

5. Sometimes pKb is used for bases. The two are related by the equation
pKa = pKb -14.
It is important to recognise that the pKa of the base is in reality the pKa of the conjugate acid (acids are proton donors HA, or protonated form, BH+) of the base.
The pKas for ephedrine and ammonia are 9.6 and 9.3 respectively. In reality this is the pKa of the protonated form, such as ephedrine hydrochloride and ammonium chloride respectively.

6. Remember that pKas indicate the extent to which the acid reacts with water to form conjugate acid and conjugate base. The equilibrium for a strong acid (low pKa) in water lies to the right favoring the formation of products (conjugate acid and conjugate base).
This means that there essentially is no unreacted HCl left in the aqueous solution of hydrochloric acid. Equilibrium for a weak acid (high pKa) lies to the left.

7. At the other extreme is ephedrine HCl with a pKa of 9. 6
At the other extreme is ephedrine HCl with a pKa of 9.6. Here the denominator representing the concentration of ephedrine HCl greatly predominate against the products, which in this example is ephedrine and H3O+.
In other words the protonated form of ephedrine is very proton donor and free ephedrine is an excellent proton acceptor.
A general rule for determining whether a chemical is a strong or weak acid or base, from pKa values, is

8. pKa less than 2: Strong acid; conjugate base has no meaningful basic properties in water
pKa 4-6: weak acid, weak conjugate base
pKa 8-10: very weak acid, conjugate base getting stronger
pKa greater than 12: essentially no acidic properties in water; strong conjugate base.

9. The values of pKa and pKb quoted in the literature tell absolutely nothing about whether the drug in question is an acid or base. These values give information about the strength of acids or bases; they tell the pH at which 50% of the drug is ionised, but they do not tell whether a drug behaves as an acid or base in solution.
Amines, for example are basic and have pKa values of approximately 9, while phenols are acidic and typically have pKa values of around 10.

10. The only way to know whether a drug is acidic or basic is to learn the functional groups that confer acidity or basicity on a molecule.
Carboxylic acids
The carboxyl group is the most commonly occurring functional group on drug molecules..
Q1: The pKas of acetic acid and ethanol are 4.7 and 16 respectively. Comment on such a difference.

11. Q2: A number of commonly used drugs are carboxylic acid derivatives
Q2: A number of commonly used drugs are carboxylic acid derivatives. These include aspirin (pKa 3.5), the anticancer compound methotrexate (pKa 3.8, 4.8 and 5.6) and the diuretic furosemide (pKa 3.9). The structures of these compounds are shown below.
Explain the difference in pKas of these compounds and comment on the degree of ionisation of these drugs at the pH of human blood. . 55

12. Phenols
Phenols are weak acids that liberate protons to give the resonance stabilised the phenoxide anion. They have pKa values of approximately 10.
A number of common drugs contain the phenol functional group. These include paracetamol, morphine and levothyroxine of pKas 9.5, 9.9 and 10 respectively. They will ionise to approximately 1% at the pH of blood

13. Warfarin is an anticoagulant drug that inhibits the clotting action of blood through an action on vitamin K-derived clotting factors. It has a pKa of 5.0 and in the free acid form is not soluble in water and is therefore admistered as the sodium salt.
Warfarin exhibits keto-enol tautomerisation. Although the enol tautomer is present in small extent, it can be used to explain the acidic properties of the drug.

14. Amines
Not all compounds containing nitrogen atom(s) are basic. Amides are neutral and quite few drugs containing nitrogen atoms are actually acidic.
Compounds are basic only if the lone pair of electrons on the nitrogen is available for reaction with protons.

15. Phenylbutazone is a NASID drug that exerts an anti-inflammatory action through inhibition of the enzyme cyclooxygenase. It is a weak acid
with pKa of 4.4.
Indometacin is another NASID with a similar mode of action to that of phenylbutazone with pKa of 4.5.

16. Barbiturates are cyclic imides used as hypnotics
Barbiturates are cyclic imides used as hypnotics. They are all derivatives of barbituric acid which is not pharmacologically active. They behave as weak acids, diprotic.
The delocalisation is similar to that of warfarin and the pKas range from 7-8 for the first ionisation and for the second ionisation. The drugs are usually administered as sodium salts to increase water solubility.

17. The sulfur analogue of pentobarbital, the thiopental, is widely used in operating theatres for the induction of general anesthesia.
When thiopental are adminisred intravenously to a vein in the back of the hand it will induce unconsciousness within a second and will last for few minutes, which is sufficient time for preparation of a patient to commence general anesthesia.

18. Phenytoin is an anticonvulsant widely used in the treatment of epilepsy. Its properties resemble those of barbiturates, pKa of 8.3 and like the barbiturates display tautomerism of imine-imide type, the imide is predominant.
Sulphonamides are antibacterial compounds, contain the sulfonamide group SO2NH. They are all weakly acidic pKa approximately 5-8. They are usually administered in the form of sodium salts to increase water solubility.

19. Basic drugs
They are usually administered as their water soluble salts ( generally the hydrochloride). Care must be taken not to coadminister anything that will raise the pH of the hydrochloride salt solution in case precipitation of the less water-soluble free base occurs.
Basicity of heterocyclic compounds
Piperidines - pKa 8-9
Pyrroles, pKa -ve - zero
Pyridines, pKa 4-5

20. Examples of calculations requiring the pKa
Ex: What is the ratio of ephedrine to ephedrine HCl (pKa 9.6) in the intestinal tract at pH 8.0?

21. The number whose log is - 1. 6 is 0
The number whose log is is 0.025, meaning that there are 25 parts ephedrine for every 1,000 parts ephedrine HCl in the intestinal tract whose environment is pH 8.0.
What is the pH of a buffer containing 0.1-M acetic acid (pKa 4.8) and 0.08-M sodium acetate?
What is the pH of a 0.1-M acetic acid solution? Use the following equation for calculating the pH of a solution containing either an HA or BH+ acid.

22. What is the pH of a 0. 08-M sodium acetate solution
What is the pH of a 0.08-M sodium acetate solution? Remember, even though this is the conjugate base of acetic acid, the pKa is still used.
The pKw term in the following equation corrects for the fact that a proton acceptor (acetate anion) is present in the solution. The equation for calculating the pH of a solution containing either an A- or B base is

23. What is the pH of an ammonium acetate solution
What is the pH of an ammonium acetate solution? The pKa of the ammonium (NH4+) cation is 9.3. Always bear in mind that the pKa refers to the ability of the proton donor form to release the proton into water to form H3O+. Since this is the salt of a weak acid (NH4+) and the conjugate base of a weak acid (acetate anion), the following equation is used. Note that molar concentration is not a variable in this calculation.

24. What is the percentage ionization of ephedrine HCl (pKa 9
What is the percentage ionization of ephedrine HCl (pKa 9.6) in an intestinal tract buffered at pH 8.0 (see example 1)? Use Equation 2.4 because this is a BH+ acid.
Only 2.4% of ephedrine is present as the un-ionized conjugate base.
What is the percentage ionization of indomethacin (pKa 4.5) in an intestinal tract buffered at pH 8.0? Use Equation 2.3 because this is an HA acid.

25. A general rule for determining whether a chemical is strong or weak acid or base
For all practical purposes, indomethacin is present only as the anionic conjugate base in that region of the intestine buffered at pH 8.0.
pKa <2: strong acid; conjugate base has no meaningful basic properties in water
pKa 4 to 6: weak acid; weak conjugate base
pKa 8 to 10: very weak acid; conjugate base getting stronger
pKa >12: essentially no acidic properties in water; strong conjugate base

26. This delineation is only approximate
This delineation is only approximate. Other properties also become important when considering cautions in handling acids and bases. Phenol has a pKa of 9.9, slightly less than that of ephedrine HCl. Why phenol is considered corrosive to the skin, whereas ephedrine HCl or free ephedrine is considered innocuous when applied to the skin? Phenol has the ability to partition through the normally protective lipid layers of the skin. Because of this property, this extremely weak acid has carried the name carbolic acid. Thus, the pKa simply tells a person the acid properties of the protonated form of the chemical. It does not represent anything else concerning other potential toxicities.

27. Percent Ionization
Using the drug's pKa, the formulation or compounding pharmacist can adjust the pH to ensure maximum water solubility (ionic form of the drug) or maximum solubility in nonpolar media (un-ionic form). This is where understanding the drug's acid-base chemistry becomes important:

28.  Acids can be divided into two types, HA and BH+, on the basis of the ionic form of the acid (or conjugate base). HA acids go from un-ionized acids to ionized conjugate bases. In contrast, BH+ acids go from ionized (polar) acids to un-ionized (nonpolar) conjugate bases. In general, pharmaceutically important HA acids include the inorganic acids (e.g., HCl, H2SO4), enols (e.g., barbiturates, hydantoins), carboxylic acids (e.g., low-molecular-weight organic acids, arylacetic acids, N-aryl anthranilic acids, salicylic acids), and amides and imides (e.g., sulfonamides and saccharin, respectively). The

29. The chemistry is simpler for the pharmaceutically important BH+ acids: They are all protonated amines. A polyfunctional drug can have several pKa's (e.g., amoxicillin). The latter's ionic state is based on amoxicillin's ionic state at physiological pH 7.4.
The percent ionization of a drug is calculated by using Equation 2.3 for HA acids and Equation 2.4 for BH+ acids.

31. Increasing the hydrogen ion concentration (decreasing the pH) will shift the equilibrium to the left, thereby increasing the concentration of the acid and decreasing the concentration of conjugate base. In the case of indomethacin, a decrease of 1 pH unit below the pKa will increase the concentration of un-ionized (protonated) indomethacin to 9.1%.
Similarly, a decrease of 2 pH units results in only 0.99% of the indomethacin being present in the ionized conjugate base form.

32. The opposite is seen for the BH+ acids
The opposite is seen for the BH+ acids. The percentage of ephedrine present as the ionized (protonated) acid is 90.9% at 1 pH unit below the pKa and is 99.0% at 2 pH units below the pKa.
With this knowledge in mind, return to the drawing of amoxicillin. At physiological pH, the carboxylic acid (HA acid; pKa1 2.4) will be in the ionized carboxylate form, the primary amine (BH+ acid; pKa2 7.4) will be 50% protonated and 50% in the free amine form, and the phenol (HA acid; pKa3 9.6) will be in the un-ionized protonated form.

33. Knowledge of percent ionization makes it easier to explain and predict why the use of some preparations can cause problems and discomfort as a result of pH extremes. Phenytoin (HA acid; pKa 8.3) injection must be adjusted to pH 12 with sodium hydroxide to ensure complete ionization and maximize water solubility. In theory, a pH of 10.3 will result in 99.0% of the drug being an anionic water-soluble conjugate base. To lower the concentration of phenytoin in the insoluble acid form even further and maintain excess alkalinity, the pH is raised to 12 to obtain 99.98% of the drug in the ionized form.

34. Even then, a cosolvent system of 40% propylene glycol, 10% ethyl alcohol, and 50% water for injection is used to ensure complete solution. This highly alkaline solution is irritating to the patient and generally cannot be administered as an admixture with other intravenous fluids that are buffered more closely at physiological pH 7.4. This decrease in pH would result in the parent un-ionized phenytoin precipitating out of solution.

35. Ionization (%)
HA Acids
BH Acids
pKa - 2 pH units
0.99
99.0
pKa - 1 pH unit
9.1
90.9
pKa = pH
50.0
pKa + 1 pH unit
pKa + 2 pH units

37. Adjustments in pH to maintain water solubility can sometimes lead to chemical stability problems. An example is indomethacin (HA acid; pKa 4.5), which is unstable in alkaline media. Therefore, the preferred oral liquid dosage form is a suspension buffered at pH 4 to 5. Because this is near the drug's pKa, only 50% will be in the water-soluble form. There is a medical indication requiring intravenous administration of indomethacin to premature infants. The intravenous dosage form is the lyophilized (freeze-dried) sodium salt, which is reconstituted just prior to use.

38. Ionization – pH Profiles
The plot of percent ionisation versus pH for an HA acid (indomethacin, pKa 4.5) and an HB+(ephedrine, pKa 9.6) illustrates how the degree of ionisation can be shifted significantly with small changes in pH. Similar sketches can made for any acid.
When the pH = pKa the compounds are 50% ionised. An increase by 1 pH unit from the pKa of indomethacin results in 90.9% but decrease the ionisation of ephedrine HCl to 9.1%.

39. This highly alkaline solution is irritating to the patient and generally cannot be administered as an admixture with other intravenous fluids that are buffered more closely at physiological pH 7.4. This decrease in pH would result in the parent unionised phenytoin precipitating out of solution.
The acidic eye drops tropicamide pKa of 5.2 can sting, pH of 4 to obtain more than 90% ionisation. Local anesthetic eye drops are used to minimise the patient's discomfort.

40. Chemical stability of a drug can sometimes be affected by pH adjustments.
An example is iodomethacin of pKa 4.5 which is unstable in alkaline media. IV dosage of the lophylised ( freeze - dried ) sodium salt, which is reconstituted just prior to use.
Drugs in an ionised form will tend to distribute by the blood throughout the body more rapidly than unionised, nonpolar, molecules.

41. In general drugs pass through the nonpolar membranes of the capillary walls, cell membranes and the blood-brain barrier in the unionised (non-polar) form.
For HA acids, it is the parent acid that will readily cross these membranes. The situation is just opposite for the BH+ acids.
The unionised conjugate base (free amine) is the species most readily crossing the nonpolar membranes, see diagrams for passage of HA and HB+ through lipid barriers

42. computer-aided drug design: early methods
Initially, the design of new drugs was based on starting with a prototypical molecule, usually a natural product and making structural modifications.
Examples include steroidal hormones based on naturally occurring cortisone, testosterone, progesterone and estrogen; adrenergic drugs based on epinephrine; local anesthetics based on cocaine; opiate analgesics based on morphine; antibiotics based on penicillin, cephalosporin and tetracycline.

43. Examples of prototypical molecules that were not natural in origin include the antipsychotic phenothiazines, bisphosphonates for osteoporosis, benzodiazepines indicated for various CNS treatments.
Although prototypical molecules have produced significant advancements in treating diseases, this approach to drug development is limited to the initial discovery of the prototypical molecule. Today, it is more common to take a holistic approach that, where possible, involves understanding the etiology of the disease and the structure of the receptor where the ligand (drug) will bind.

44. Increasing computer power coupled with applicable software, both at reasonable cost, has led to more focused approaches for the development of new drugs. Computational methodologies include mathematical equations correlating structure with biological activity, searching chemical databases for leads and rapid docking of ligand to the receptor. The latter requires 3D structure information of the receptor. Originally crystallized enzymes were the common receptors, and their spatial arrangements determined by x-ray crystallography. Today's software can calculate possible 3D structures of protein starting with the amino acid sequence.

45. There are many strategies in the design of a drug such that the new drug has a better fit for its desired target binding site. Other strategies involve change in functional groups or substituents such that the drug's pharmacokinetics or binding site interactions were improved.
These strategies involve the synthesis of analogue containing a range of substituents. Because there will be a large number of combinations. A rational approach is QSAR.

46. QSAR attempts to identify and quantify the physiochemical properties of a drug and to check whether any of these properties has an effect on the biological activity.
QSAR equations tell about the role of the property on pharmacokinetics or mechanism of drug action. It allows predication of the biologictivity of similar combinations. It also allows, in advance, the calculation of the biological activity of a novel analogue

47. Because a large number of physiochemical properties may affect the biological activity of a drug and the difficulties involved in quantifying them, a practical approach is to vary one or two properties while keeping the others constant. However, some changes may affect more than one property at the same time.
When using QSAR the compounds studied must be related structurally, act on the same target and have the same mechanism of action. In vitro testing of activity is more reliable than in vivo testing due to complications involved.

48. A graph is drawn of biological activity (log 1/C) versus the physiochemical property e.g log P. The line of best fit through the data points is drawn. Regression coefficients r2 is often quoted with values over 0.8 are considered a good fit. For example a value of r2 signifies that 90% of the drug's activity is accounted for by that property. The larger the number of compounds, the more meaningful r2 will be. It is also common to report the standard deviation ,s, which tells about the experimental error in the physiochemical property determination. It is also a common practice to quote p values derived from F-tests.

49. A value of p = 0.05 means the parameter is significant otherwise it should not be included in the QSAR equation.

50. QSAR, Goals
Just as mathematical modeling is used to explain and model many chemical processes, it has been the goal of medicinal chemists to quantify the effect of a structural change on a defined pharmacological response. This would meet three goals in drug design:
(a) to predict biological activity in untested compounds,
(b) to define the structural requirements required for a good fit between the drug molecule and the receptor, and
(c) to design a test set of compounds to maximize the amount of information concerning structural requirements for activity from a minimum number of compounds tested.

51. QSAR aspect of medicinal chemistry is commonly referred to as quantitative structure-activity relationships (QSAR).
The goals of QSAR studies showed that the gradual chemical modification in the molecular structure of a series of poisons produced some important differences in their action.
The physiological action, ¢, of a molecule is a function of its chemical constitution, C.
¢ = k C where k is constant

52. The problem now becomes one of numerically defining chemical structure
The problem now becomes one of numerically defining chemical structure. It still is a fertile area of research. What has been found is that biological response can be predicted from physiochemical properties. The latter includes;
Hydrophobic parameters , Electronic effects, Steric factors, Molar refractivity, Hydrogen bonding, Dipole moments, Interatomic distances, vapor pressure, water solubility,
However, it is important to note that some of these parameters are difficult to quantify.

53. Partition Coefficient
It was clear from drug distribution studies how important hydrophobicity of a drug is in especially in partisioning and in drug receptor interaction. The most common physicochemical descriptor is the molecule's partition coefficient in an octanol/water system. The drug will go through a series of partitioning steps:
leaving the aqueous extracellular fluids.

54. passing through lipid membranes.
entering other aqueous environments before reaching the receptor. In this sense, a drug is undergoing the same partitioning phenomenon that happens to any chemical in a separatory funnel containing water and a nonpolar solvent such as hexane, chloroform, or ether.

55. The partition coefficient (P) is the ratio of the molar concentration of chemical in the nonaqueous phase (usually 1-octanol) versus that in the aqueous phase. For reasons already discussed, it is more common to use the logarithmic expression. The difference between the separatory funnel model and what actually occurs in the body is that the partitioning in the funnel will reach an equilibrium at which the rate of chemical leaving the aqueous phase and entering the organic phase will equal the rate of the chemical moving from the organic phase to the aqueous phase.

56. This is not the physiological situation
This is not the physiological situation. Dynamic changes are occurring to the drug, such as it being metabolized, bound to serum albumin, excreted from the body, and bound to receptors. The environment for the drug is not static. Upon administration, the drug will be pushed through the membranes because of the high concentration of drug in the extracellular fluids relative to the concentration in the intracellular compartments. In an attempt to maintain equilibrium ratios, the flow of the drug will be from systemic circulation through the membranes onto the receptors. As the drug is metabolized and excreted from the body, it will be pulled back across the membranes, and the concentration of drug at the receptors will decrease.

57. assume that the drug is in the nonpolar state
assume that the drug is in the nonpolar state. A large percentage of drugs are amines whose pKa is such that at physiological pH 7.4, a significant percentage of the drug will be in its protonated, ionized form. A similar statement can be made for the HA acids (carboxyl, sulfonamide, imide) in that at physiological pH, a significant percentage will be in their anionic forms. An assumption is made that the ionic form is water-soluble and will remain in the water phase of an octanol/water system. This reality has led to the use of log D, which is defined as the equilibrium ratio of both the ionized and un-ionized species of the molecule in an octanol/water system.

58. Because much of the time the drug's movement across membranes is a partitioning process, the partition coefficient has become the most common physicochemical property. The question that now must be asked is what immiscible nonpolar solvent system best mimics the water/lipid membrane barriers found in the body? It is now realized that the n-octanol/water system is an excellent estimator of drug partitioning in biological systems. One could argue that it was fortuitous that n-octanol was available in reasonable purity for the early partition coefficient determinations. To appreciate why this is so, one must understand the chemical nature of the lipid membranes.

59. These membranes are not exclusively anhydrous fatty or oily structures
These membranes are not exclusively anhydrous fatty or oily structures. As a first approximation, they can be considered bilayers composed of lipids consisting of a polar cap and large hydrophobic tail. Phosphoglycerides are major components of lipid bilayers. Other groups of bifunctional lipids include the sphingomyelins, galactocerebrosides, and plasmalogens. The hydrophobic portion is composed largely of unsaturated fatty acids, mostly with cis double bonds. There is poor correlation between the partition coefficient of a series of molecules and the biological response

60. These m embranes are not exclusively anhydrous fatty or oily structures. As a first approximation, they can be considered bilayers composed of lipids consisting of a polar cap and large hydrophobic tail. Phosphoglycerides are major components of lipid bilayers. Other groups of bifunctional lipids include the sphingomyelins, galactocerebrosides, and plasmalogens. The hydrophobic portion is composed largely of unsaturated fatty acids, mostly with cis double bonds. There is poor correlation between the partition coefficient of a series of molecules and the biological response.

61. General structure of a bifunctional phospholipid
General structure of a bifunctional phospholipid. Many of the fatty acid esters will be cis unsaturated.
Schematic representation of the cell membrane.

62. There are receptors on the cell surface where hormones such as epinephrine and insulin bind, setting off a series of biochemical events within the cell. Some of these receptors are used by viruses to gain entrance into the cells, where the virus reproduces. As newer instrumental techniques are developed, and genetic cloning permits isolation of the genetic material responsible for forming and regulating the structures on the cell surface, the image of a passive lipid membrane has disappeared to be replaced by very complex, highly organized, dynamically functioning structure.

63. For purposes of the partitioning phenomenon, picture the cellular membranes as two layers of lipids. The two outer layers, one facing the interior and the other facing the exterior of the cell, consist of the polar ends of the bifunctional lipids. Keep in mind that these surfaces are exposed to an aqueous polar environment. The polar ends of the charged phospholipids and other bifunctional lipids are solvated by the water molecules. There are also considerable amounts of charged proteins and mucopolysaccharides present on the surface. In contrast, the interior of the membrane is populated by the hydrophobic aliphatic chains from the fatty acid esters.

64. With this representation in mind, a partial explanation can be presented as to why the n-octanol/water partitioning system seems to mimic the lipid membranes/water systems found in the body. It turns out that n-octanol is not as nonpolar as initially might be predicted. Water-saturated octanol contains 2.3 M water because the small water molecule easily clusters around octanol's hydroxy moiety. n-Octanol-saturated water contains little of the organic phase because of the large hydrophobic 8-carbon chain of octanol.

65. The water in the n-octanol phase apparently approximates the polar properties of the lipid bilayer, whereas the lack of octanol in the water phase mimics the physiological aqueous compartments, which are relatively free of nonpolar components. In contrast, partitioning systems such as hexane/water and chloroform/water contain so little water in the organic phase that they are poor models for the lipid bilayer/water system found in the body.

66. At the same time, remember that the n-octanol/water system is only an approximation of the actual environment found in the interface between the cellular membranes and the extracellular/intracellular fluids.
Experimental determination of octanol/water partition coefficients is tedious and time consuming. Today, most are calculated. The accuracy of these calculations is only as good as the assumptions made by the writers of the software. These include atomic fragment values, correction factors, spatial properties, effects of resonance and induction, internal secondary bonding forces, etc.

67. Quantitative Structure-Activity Relationship Study
Compound
Log 1/BR
1/BR BR
BRx1000
Log1/BR
LogPC
PCx0.01
Chlorpromazine
5.20
4.22
Propoxyphene
5.0
-5.080
2.3
Amitriptyline
4.9
-4.920
2.5
Dothiepin
4.7
-4.750
2.7
Secobarbita
4.1
-4.190
1.9
Phenobarbita
3.7
5128.6
-3.710
1.1
Chloroform
3.6
3981.0
-3.600
Chlormethiazol
3.5
3235.9
-3.510
2.1
Paraldehyd
2.8
758.5
2.880
0.6
Ether
2.17
147.9
-2.170
0.8
Ethanol
1.0
11.4
-1.060
-0.3
Quantitative Structure-Activity Relationship Study

68. A study of a group of griseofulvin analogues showed a linear relationship between the biological response and both lipophilicity (log P) and electronic character (σ). It was suggested that the antibiotic activity may depend on the enone system facilitating the addition of griseofulvin to a nucleophilic group such as the SH moiety in a fungal enzyme.

69. A parabolic relationship was reported for a series of substituted acetylated salicylates (substituted aspirins) tested for anti-inflammatory activity. A nonlinear relationship exists between the biological response and lipophilicity, and a significant detrimental steric effect is seen with substituents at position 4. The two sterimol parameters used in this equation were L, defined as the length of the substituent along the axis of the bond between the first atom of the substituent and the parent molecule, and B2, defined as a width parameter. Steric effects were not considered statistically significant at position 3, as shown by the sterimol parameters for substituents at position 3 not being part of equation

70. The optimal partition coefficient (log Po) for the substituted aspirins in this assay was 2.6. At the same time, increasing bulk, as measured by the sterimol parameters, decreases activity.

71. Let us assume that a new series of drug molecules is to be synthesized based on the following structure. The goal is to test the effect of the 16-substituents at each of the three positions on our new series. The number of possible analogs is equal to 163, or 4,096 compounds, assuming that all three positions will always be substituted with one of the substituents. If hydrogen is included when a position is not substituted, there are 173, or 4,913, different combinations.

72. The problem is to select a small number of substituents that represent the different ranges or clusters of values for lipophilicity, electronic influence, and bulk. An initial design set could include the methyl and propyl from the aliphatic cluster, fluorine and chlorine from the halogen cluster, N-acetyl and phenol from the substituents showing hydrophilicity, and a range of electronic and bulk values. Including hydrogen, there will be 73, or 343, different combinations. Obviously, that is too many for an initial evaluation. Instead, certain rules have been devised to maximize the information obtained from a minimum number of compounds. These include the following:

73. Each substituent must occur more than once at each position on which it is found.
The number of times that each substituent at a particular position appears should be approximately equal.
No two substituents should be present in a constant combination. When combinations of substituents are a necessity, they should not occur more frequently than any other combination.
Following these guidelines, the initial test set can be reduced to 24 to 26 compounds.

74. Today, the partition coefficient has become the single most important physical chemical measurement for QSAR studies. The equation for a straight line (y = mx + b) where BR =; a defined pharmacological response usually expressed in millimoles such as the inhibitory constant Ki, the effective dose in 50% of the subjects (ED50), the lethal dose in 50% of the subjects (LD50), or the minimum inhibitory concentration (MIC).  It is common to express the biological response as a reciprocal, 1/BR or 1/C, a = the regression coefficient or slope of the straight line, c = the intercept term on the y axis (when the physical chemical property equals zero)

75. To understand the concepts in the next few paragraphs, it is necessary to know how to interpret defined pharmacological concepts such as the ED50, which is the amount of the drug needed to obtain the defined pharmacological response in 50% of the test subjects.
Let us assume that drug A's ED50 is 1 mmol and drug B's ED50 is 2 mmol. Drug A is twice as potent as drug B. In other words, the smaller the ED50 (or ED90, LD50, MIC, etc.), the more potent is the substance being tested.

76. The logarithmic value of the dependent variable (concentration necessary to obtain a defined biological response) is used to linearize the data. QSARs are not always linear.
Nevertheless, using logarithms is an acceptable statistical technique (taking reciprocals obtained from a Michaelis - Menton study produces the linear Line weaver-Burke plots found in any biochemistry textbook).

77. Now, why is the biological response usually expressed as a reciprocal
Now, why is the biological response usually expressed as a reciprocal? Sometimes, one obtains a statistically more valid relationship. More importantly, expressing the biological response as a reciprocal usually produces a positive slope.
Q1: Comment on the QSAR for
(i) the binding of 42 compounds to serum albumin which is given as,
Log (1/C) = 0.75logP (n= 42, r = 0.960, s = 0.159).

78. (ii) the general anesthetic activity for a range of ethers was given by
Log (1/C) = (log P) log P
Note: when different classes of anesthetics are used the equations were similar, parabolic, but have different constants. However, log Po for the optimum activity was 2.3. This means that anesthetics are operating on a similar fashion i.e. there are no specific drug-receptor interaction and the mechanism of the drug is controlled purely by its ability to enter cell membranes.

79. Furthermore, since different anesthetics have similar log Po values, the log P value of any drug can give some idea of potential potency as an anesthetic. It also means that drugs which are to be targeted for CNS should have log P value of about 2. This implies that drugs with log P values different than 2 are not expected to cause drowsiness.

80. While log P of a compound can be found experimentally
While log P of a compound can be found experimentally. Theoretical values can be calculated from substituent hydrophobicity constants, π, and decide in advance whether a compound is worth synthesizing.
Q2: Calculate Log P for m-chlorobenzimide.
The main difference between using π instead of log P is that it refers to the activity of a part of the compound rather than the whole compound.

81. Electron- withdrawing substiuents have positive value while electron-donting groups have negative δ values e.g. ethyl and CN- have and 0.53 respectively. The difference between ester hydrolysis under acidic and basic conditions allows steric factors to be determined as acidic conditions only steric factors are involved.
Resonance and inductive effects of a substituent are taken into account.

82. Therefore the position of the substituent is important to mention
Therefore the position of the substituent is important to mention. δ cannot be measured for ortho substituent because steric effects are involved. QSAR studies lacking π indicates the drugs do not operate by mechanisms that involve membrane crossing. An example is the antisecticidal activity of diethyl phenyl phosphate.
Log (1/C) δ
The absence of π parameter indicates these drugs do not have to pass through cell membrane to have activity. This confirmed by the finding that these drugs act on an enzyle called actylcholinesterase which is situated on the outside of the cell memberane.

83. Electronic Effects
The electronic features of a substituent directly affect partitioning of a drug through membranes and its binding to receptors. The electron with-drawing or donating ability of a substituent on a ring is usually measured as δ, Hammett substituent constant. The reference reaction used to determine value was the dissociation of benzoic acids compared to the acid itself. The stabilization of the anion is the main factor.
Aliphatic substituent constants are determined from the rate of hydrolysis of a series aliphatic esters as compared to the parent unsubstituted ester. In this case the δ is purely inductive.

84. Steric Factors
A bulky group might act as a shield and hinder the binding between a drug and its receptor. However, it may help in the orientation of a drug properly for maximum binding activity.
Taft's steric factors obtained from the rates of hydrolysis of substituted esters as compared to the unsubsustituted compound as Es = log ks - log ko

85. Substituents like H and F results with rates faster (positive values) than bulky groups.
Molar refractivity, MR
MR is a measure of the volume occupied by the substituent. It is obtained from the following equation;
MR = (n2-1)/ (n2+2) x MW/d
Verloop steric parameters can be measured using the computer software, Sterimol. Bond lengths, van der Waal's radii, bond angles and possible conformation of the substituents are used.

86. Hansch Equation
The biological activity of most drugs is related to a combination of physiochemical properties. Hansch equations relate biological activity of to the most commonly used properties. Log (1/C) = k1 log P + k2δ + k3Es + k4
If Log P values are spread over range, the equation will be parabolic.
Log (1/C) = k1 ( log P )2 + k2 log P + k3δ + k4 Es + k5

87. Table: Physiochemical Parameters for QSAR
Substituent π
δ meta
δ para -H
0.00
-CH3
0.56
-0.07
-0.17
-CH2 CH3
1.02
-0.15
- CH2 CH2CH3
1.55
-0.13
-C(CH3)2
1.53
-π0.07
-OCH3
-0.02
0.12
-0.27
-NH2
-1.23
-0.16
-0.66 -F
0.14
0.34
0.06
-Cl
0.71
0.37
0.23
-Br
0.86
0.39 -I
1.12
0.35
0.18
-CF3
0.88
0.43
0.54
-OH
-0.67
-0.37
-COCH3
-0.55
0.38
0.50
-NHCOCH3
-0.97
0.21
-NO2
-0.80
0.78
-CN
-0.57
0.66

88. Example:
The QSAR for a series of phenanthrene aminocarbinols was test for antimalarial activity with X and Y and represent benzene rings on the left and right.
Log (1/C) = (πsum) πsum ∑ πx ∑ πy ∑ δx+ 0.88∑ δy+ 2.34
(n =102, r = 0.913, r2 = 0.834, s= 0.258)

89. Graig Plot
It is easier to visualize graphs than tables. An example is to plot δ and π factors on the x and y- axes respectively. The advantages of such plots include;
Graig plot are scattered.
The plots make it easy to see which substituents have similar parameter and how to vary them to achieve better QSAR equation.
Plots show whether π and or δ should be positive or negative for better activity as the required by QSAR equations.

90. Q1: Given log P for benzene = 2
Q1: Given log P for benzene = 2.13, use table of physiochemical properties to calculate log P value for;
m-methylphenol, p- ethyltoluene
salicylic acid, benzoic acid
menadione , paracetamol
aspirin, with -COOH and o-OCOCH3

91. Q2: Calculate the pH of the following solutions;
0.1M ephedrine hydrochloride, Ka 2.5x10-10
0.01 M indomethacin, pKa = 4.5.
Q3: Calculate the % ionization of a drug that contains a basic nitrogen of pKa 9 at;
Empty stomach, pH= 2, Full stomach, pH = 6, Plasma
Large intestine
Q5: Identify acidic /basic groups in paracetamol, phenol with p-NHCOCH3
Q5: Sketch % ionization-pH profile for;
Menadione, Paracetamol

92. Topological Descriptors
This method is based on graph theory, in which atoms connecting the atoms are considered a path that is traversed from one atom to another. Hydrogen – suppressed graph representation is used to calculate the sum of possible path routes from individual atoms using the formula of reciprocal square root of the number of bonds connecting individual atoms. The sum of path routes is found from reciprocal square of the products of each path. Modifications are made to differentiate atoms e.g. a hydroxyl and an amine and their environments within a molecule. An example of using this method is explained in the literature.

93. However, it is difficult to interpret the meaning of these topological indices as they are correlated with all physiochemical descriptors. It is also difficult to make a decision as what molecular modifications can be made to enhance activity further.
In this method is based on identifying physiochemical parameters and structural attributes that contribute to a class or type of biological activity. The compounds are classified into grouping such as carcinogenic/ noncarcenogenic, sweet/bitter, active / inactive, and depressant/stimulant. The software in the computer programs breaks the molecule down into substructures e.g. carbonyls, enones, conjugations, rings of different sizes and types, and N-substitution patterns. The latter become variables that may be used.

94. Classification Methods
In this method is based on identifying physiochemical parameters and structural attributes that contribute to a class or type of biological activity. The compounds are classified into grouping such as carcinogenic/ noncarcenogenic, sweet/bitter, active / inactive, and depressant/stimulant.
The software in the computer programs breaks the molecule down into substructures e.g. carbonyls, enones, conjugations, rings of different sizes and types, and N-substitution patterns. The latter become variables that may be used.

95. Classification Methods
Training set containing large number of chemicals well characterized in terms of biological activity will be established. An example for the successful application of this technique used tranquillizers versus sedatives. Sixty nine descriptors were used to characterize the molecules. Recently, databases of existing compounds are scanned for molecules that possess what appears to be the desired parameters

96. Thank You