Quantitative Structure Activity Relationships (QSAR) We have already seen that by changing groups in a drug may increase or decrease

e the activity, especially in terms of receptor binding interactions. Structural changes may also effect drug distribution, metabolism, or stability. Thus, in order to alter such properties in a logical and predictable fashion, we must consider a brief understanding of QSAR. As a result, we may be able to address more precisely how to circumvent drugs with pharmacokinetic shortcomings. Understanding structure-activity relationships can be done by trial and error for each particular drug or chemical system under consideration. However, a more logical and generalized approach may prevent ignorant reinventions and would be useful in predicting desired outcomes (i.e., increased stability , decreased side effects, increased water solubility or lipophilicity). Ideally, QSAR will provide a method to quantify a linear relationship between a physicochemical property or a drug and its biological activity. What properties would we be interested in? Well, structural, physical, and chemical properties cover most all issues of concern for a drug. In this section, we will gain an understanding of QSAR regarding electronic and steric effects as well as lipophilicity.

Linear Free Energy Relationships allow a correlation of substituents with a reaction rate, biological activity, pKa, etc. To help us understand the magnitude of the sensitivity of reaction to changing substituents, we need a reference reaction. This is precisely what Hammett set out to accomplish. Hammett Equation (Electronic Effects) relates reaction rates with acid dissociation constants. Consider the following dissociation of a substituted benzoic acid.
O OH O

Ka
X

Ka = dissociation constant Ka0 = dissociation constant when X = H

 Ka = dissociation constant Ka0 = dissociation constant when X = H

X

O OH

Ka
X

Lets consider a few different types of X-groups compared to H. If X = EWG, the carboxylate ion is stabilized more than when X = H As a result, Ka increases (compared to when X = H) If X = EDG, the carboxylate ion is less stabilized than when X = H. As a result, Ka decreases (compared to when X = H) Thus, we can make measurements of Ka for many different substituents and then make the following definition. log Ka/Ka0 = (sigma)

When X = H, Ka = Ka0 and log Ka/Ka0 = = 0. When X = EWG, Ka > Ka0 and > 0 (+ value) When X = EDG, Ka < Ka0 and < 0 (- value)

Therefore, depends upon electronic properties of the substituent and its position. is also known as substituent constant. When the substituent X is in the meta position on the aromatic ring, the effect is mostly inductive. However, when the substituent X is in the para position, both inductive and resonance effects are contributing. O
OH X X

O OH

Therefore, meta and para are generally not the same for the same substituent. ortho are more difficult to measure and simply quantify due to steric effects on the reactive portion of the molecule. Calculating a few values should provide a further appreciation. Ka 3.45x10-4 6.46x10-5 3.38x10-5 = log (3.38x10-5 / 6.46x10-5) = -0.28

X = meta-NO2 X=H X = para-CH3O

= log (3.45x10-4 / 6.46x10-5) = 0.73

 March, p. 244 (sigma m and p only)

Now that weve identified our reference reaction (i.e., dissociation of substituted benzoic acids) lets compare it to a different systems.
A
C O2 H

Ka
X

C O2

Remember that Ka0 is for when X = H.

B
X

C O2 H

Ka
X

C O2

If we plot log (Ka/Ka0) for these dissociation reactions vs. the values obtained from our reference reaction, we should see similar trends but perhaps to a different extent as the X-group is now further away from the business portion of the molecule.

From these plots we also get more information. We now can compare the slopes for different reactions and draw more conclusions. First we must define the slope = (rho) For our reference reaction, (dissociation of benzoic acids) = 1. This is because we would be plotting log (Ka/Ka0) for substituted benzoic acids vs. values. But remember, = log (Ka/Ka0) for substituted benzoic acids!

then becomes a measure of a reactions sensitivity to electronic effects. The further away the substituent is from the reaction center, the weaker the effect and thus <1 but still greater than 0 as long as EWG increase the extent (or rate) of reaction and EDG decrease the extent (or rate) of the reaction.

So how does this effect activity of our drugs? Consider that an amine may be protonated in a receptor and must be so to form ionic interactions with the receptor. Thus if you want to maximize the interactions of your drug with the receptor, you can now logically select which X-groups would be beneficial.
NH3
+

Ka
X

NH2

Should one select a substituent with a that is + or in this case? Would the sign of be + or ?

Hammett also considered reaction rates as well as dissociation constants. Specifically, he examined the alkaline hydrolysis of substituted ethyl benzoates.
O O OEt

k is the rate constant for X k0 is for when X = H

X

k
HO
-

EtOH

Again, EWG (+ values) will increase the rate of reaction as the carboxylate ion is stabilized by such groups. Of course, EDG will slow the reaction down. Therefore, the slope (or the value should remain positive).

doesnt need to be positive. We could imagine a reaction where EWG would decrease the rate or extent of reaction. Consider the acid hydrolysis of an amide (perhaps in the stomach?). If the rate limiting step is the protonation of the carbonyl oxygen, how do substituents effect this step? We would expect that EDGs would favor this step. As a result, the value should be negative! In fact = -0.483 for this reaction. So how would you use this information if you wanted to increase the stability of your drug in the stomach??
O NHR H
+

O OH + H NR 2

H2O X
+

H O NHR H2 O X X O H O

H O NHR H H X O

NHR H

QSAR In conclusion provides a measure of the sensitivity to electron donation or withdrawal may be (+) or (-). If = (+); the reaction rate is increased by EWG If = (-); the reaction rate is increased by EDG The magnitude of is dependent upon the distance of the substituent from the reaction center (or the sensitivity to substituent effects).

What about steric effects on reactions?

The Taft Equation (Es) In the 1950s, Taft proposed that Linear Free Energy Relationships could be extended to include steric factors. The reference reaction that he utilized was the acid-catalyzed hydrolysis of substituted methyl acetates.

O X OCH3

k
H , H2 O
+

O X OH + HOCH 3

The Steric Contribution Es was defined by the following equation which should seem similar to that for sigma values for electronic effects discussed previously. Es = log (k X-COOMe / kMe-COOMe) The reference substituent was chosen to be X = CH3. In this case any group larger than CH3 should give a () A group smaller (i.e., X = H) gives a (+) value.

O X OCH3

k
H , H2 O
+

O X OH + HOCH 3

Es = log (kX-COOMe / kMe-COOMe)

Group H Me Et ClCH 2 n-Pr n-Bu n-Pentyl PhCH2 cyclo-C5H9 cyclo-C6H11 i-Bu

Es +1.24 0 -0.07 -0.19 -0.36 -0.39 -0.40 -0.38 -0.51 -0.79 -0.93

Group (Me)(Et)CH cyclo-C7H12 (Me)(Ph)CH t-Bu t-BuCH2 (Ph)2CH (Br)2CH (Et)2CH Cl3C (i-Bu) 2CH (Br)3C (Me)2(t-Bu)C (Et)3C

Es -1.13 -1.10 -1.19 -1.54 -1.74 -1.76 -1.86 -1.98 -2.06 -2.47 -2.43 -3.9 -3.8

Hydrophobicity Constant () Sometimes it may be useful to be able to predict the lipophilicity (or hydrophobicity) of a compound similar to steric and electronic effects. Hansch derived substituent constants for the contribution of atoms or groups on lipophilicity or more specifically, partition coefficient (P) Why is the partition coefficient important? Hydrophobicity may effect a drugs ability to cross cell membranes or receptor binding interactions. P is defined by the following equation. P = [compound]octanol / [compound]water

Hydrophobic compounds (nonpolar) favor solution in octanol Hydrophilic (polar) compounds favor solution in water. Hydrophobic compounds will have a LARGE P and Hydrophilic compounds will have a small P.

 How is P related to biological activity? If we let C = concentration of drug needed to achieve a desired pharmacological effect, we can express biological activity as 1/C. As a result, a low C would have a GREATER effect. In general, we find that increased hydrophobicity causes an increase in biological activity. This most probably due to the fact that drugs need to pass across membrane barriers to reach the target site. Thus, we should expect a linear correlation of biological relationship vs. hydrophobicity. On the contrary, we observe a parabolic relationship.

Old Patrick, p.132

Why do we see such a relationship? There are 3 major reasons to account for this. Drugs that are too hydrophobic are not soluble in the aqueous phase Drug trapped in fat deposits and never reach site of action Hydrophobic drugs may be more susceptible to degradative metabolism So, back to Hanschs hydrophobicity constant (). How could it be useful? Well first we need to define this constant. Hansch defined the hydophobicity constant () by the following equation. log (PX / PH) = PX is the partition coefficient of a compound containing substituent X PH is the partition coefficient for the parent (or unsubstituted) drug. Substituents that increases the hydrophobicity (or lipophilicity) of a compound will have (+) values Substituent that decrease the hydrophobicity (or lipophilicity) of compound will have (-) values.

Silverman, p.32

The Craig Plot Weve discussed electronic, steric, and hydrophobic effects and perhaps it would be useful to combine and display this information. Such a presentation is called a Craig Plot. Often you w ill see values for and plotted together as in the following graph.

Silverman, p.41

The Craig Plot The advantage to such a plot is that one may quickly identify substituents with similar electronic effects but vary in hydrophobic effects. Conversely, substituents with similar values with differing values can be just as easily identified. Thus, if one is looking for a substituent to cause a specific change in a property of a drug, a logical choice can be made. It should be noted that other Craig Plots may be generated for P, Es, etc.

Topliss Decision Tree

Useful when it is not feasible to make a large range of structures. Based upon hydrophobicity () and electronic () factors. Small library of analogs are prepared in a logical sequence: a phenyl ring of a lead compound is systematically substituted with a number of functional groups.

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Case Study: Inhibition of Prostate Specific Membrane Antigen

PSMA is a 100 Kda glycoprotein with elevated expression in prostate epithelial tissue PSMA is a transmembrane protein: 19aa cytoplasmic N-terminus, 24aa transmembrane, and 707 extracellular domain. PSMA has been observed to be expressed in neovasculature of a wide range of tumors but NOT is detected in the vasculature of benign tissue. PSMA expression in tumor tissue increases as prostate tumor grade increases. >85% DNA sequence homology to NAALADase

Known Enzymatic Activities of PSMA

Hydrolytic cleavage and liberation of glutamic acid from gamma-glutamyl derivatives of folic acid Hydrolytic cleavage and liberation of glutamic acid the neuropeptide NAAG (N-acetylaspartylglutamate).
O N H CO2 H H N O NAAG CO2 H

CO2 H PSMA

O N H

CO2 H + CO2 H

H2 N

CO2 H

CO2 H NAA Glu O OH N H N H O O CO2 H n-1 N H CO2 H CO2 H H N

O OH N H2 N N N N N H N H

CO2 H H N O Folic Acid O n N H CO2 H CO2 H H2 N CO2 H PSMA H2 N

N N +

N N

CO2 H CO2 H

CO2 H Glu

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12

Inhibition of PSMA by Hydrophobic-Probing Phosphonamidates

Inhibition of PSMA by Phenylalkylphosphonamidates

50 45

H N O NAAG

O N H CO2 H

CO2 H

v (pmol/min)

40 35 30 25 20 15 10 5 0

CO2 H

O HO P N n H

CO2 H

n = 0,1,2,3,4
no inhibitor 0 1 2 3 4

CO2 H

methyene units of alkyl tether [sub] =10 uM, [inhib] = 1 uM

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PhenylEthylPhosphonamidate Inhibitors of PSMA (Topliss Approach)

Phenyl Ethyl Analaogs (Topliss Approach)
H 3CO

% of Contraol (PSMA activity)

120.00 100.00 80.00 60.00 40.00 20.00

O

O O P OH N H OH

OH O

O O P OH N H OH
H 3C O O OH N H P OH O P OH N H

Cl

O OH

OH O

OH

OH O

0.00 no inhibitor Ph-CH24-Cl 4-Ome 4-Me Phenyl Ethyl analogs (10uM)

Research Topics & Related Resources

Consider the following concepts as you investigate your drug. Chemical structure Discovery, Isolation, and/or Synthesis Classification or Therapeutic Category Mechanism of Action Structure-Activity Studies Administration (iv, oral, etc.), Distribution Metabolism, Elimination Side Effects/Toxicity Analog Development (the next generation?)

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Research Topics & Related Resources

Searchable Databases PubMed is the National Library of Medicine's search service that provides access to over 10 million citations in MEDLINE, PreMEDLINE, and other related databases, with links to participating online journals. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi More of the National Library of Medicine's library services and its databases are here: http://www.nlm.nih.gov/libserv.html http://www.nlm.nih.gov/databases/databases.html Specifically, you may want to check out these: ChemIDplus for chemical structures, synonyms, and more. Be sure to click on the Full Record link after your search: http://chem2.sis.nlm.nih.gov/chemidplus/chemidlite.jsp TOXNET, a cluster of databases on toxicology, hazardous chemicals, and related areas: http://toxnet.nlm.nih.gov

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Searchable Databases ChemWeb (free membership) http://chemweb.com/ Databases containing abstracts, chemical structures, patents, websites and more Beilstein Abstracts Medline PharmaSource (structures!) ChemDex Plus - searchable and reviewed database of chemistry resources on the Web. ChemFinder is a chemical database. , It can also provide information such as physical property data and 2D chemical structures. http://chemfinder.cambridgesoft.com/ Web Of Science provides access to the ISI Citation Databases, which cover over 8,000 international journals. You can find this through our Librarys database listing or link here through your SFSU account: http://0-isi10.isiknowledge.com.opac.sfsu.edu:80/portal.cgi/wos STN Easy (get your login id and password from library reference desk). Search the Chemical Abstracts for chemistry references and chemical substances. http://stneasy.cas.org

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Research Topics & Related Resources

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