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Printed in the USA. All rights reserved. 0 1983 Drug Information Association Inc.
Quantum mechanics is especially useful in drug design when the mode of action of
the drug involves a chemical reaction. Some advantages as well as caveats about the
role of quantum mechanics in molecular modeling are reviewed.
that human psychotomimetic activity of where one wants t o obtain accurate infor-
amphetamine analogs is related to their ion- mation about some large drug molecules.
ization potential. Correlations were found Not infrequently the molecules are much
because the orbital energies reflect the elec- too big to determine every structural variable
tron-richness of the aromatic ring. by ab initio calculations, that is, quantum
Quantum mechanics is especially well mechanical calculations based only on first
suited to deal with transition states and principles and without empiricism.
electronically excited molecules. Sometimes One can start out by doing ab initio cal-
in drug design one is attempting to arrive culations on simple model structures that
at a transition state inhibitor. That is, one contain the functional groups of interest.
wants a molecule that is structurally and This will give the optimized internal geo-
electronically similar to a transition state metry, i.e., the equilibrium bond lengths,
formed by an enzyme’s natural substrate. bond angles, and torsional angles. Addi-
The enzyme will mistake the analog for its tionally, information is obtained about
substrate and be inhibited when the analog charges on atoms and about the potential
is able to bind at the active site more strong- energy surface, such as how much energy
ly than the substrate can. Quantum me- is required to deform or twist a bond.
chanics, especially at the more sophisticat- With this information in hand, one can
ed levels, can provide good representations next do molecular mechanics calculations
of the structural and electronic properties on the model structures and empirically ad-
of even short-lived species. just the force constant parameters until the
Finally, there is the matter of theoretical ab initio results are adequately reproduced.
rigor. Quantum mechanics is firmly based on The collection of parameters and empirical
the Schrodinger equation. As stated in Burk- energy functions, called the “force field,”
ert and Allinger’s Molecular mechanic^,^ can then be used to determine the three-
dimensional structure of conformations of
For calculating molecular properties, quantum the large molecules. The speed of these mo-
mechanics seems to be the obvious tool t o use. lecular mechanics calculations allows the
Calculations that d o not use the Schrodinger whole grid of conformational space to be
equation are acceptable only t o the extent that spanned if one desires. Finally, the atomic
they reproduce the results of high level quantum
coordinates for selected conformations of
mechanical calculations.
special interest can be fed into a quantum
mechanical program to obtain the informa-
Some theoretical purists like to emphasize
that molecular mechanics is nothing more tion that one was after to begin with.
than a fancy interpolative scheme. How-
ever, other theoreticians feel that there is QUANTUM MECHANICAL METHODS
a physical justification behind the seeming-
ly ad hoc prescription of the molecular There is a plethora of quantum mechanical
mechanics formalism. What really matters, programs available to the scientific com-
of course, is whether the results are useful. munity. Fortunately, most of these can be
obtained for just a nominal charge from the
In that light, both quantum mechanics and
Quantum Chemistry Program Exchange
molecular mechanics can provide informa-
tion helpful to drug design. (QCPE) at Indiana University.’
At the Lilly Research Laboratories,’O the
semiempirical molecular orbital (MO) pro-
SYNERGISM grams that we have found useful from time
The two approaches - quantum mechanics to time include EHT (Extended Huckel
and molecular mechanics -can even help theory), CND0/2 (complete neglect of dif-
each other. Consider the common situation ferential overlap), INDO (intermediate neg-
1 EH
CNDO12
INDO
(PCILO)
MINDO13
Calculated
Properties
Relative Total Energies
Orbital Energies
lonization Potentials
Charges
Dipole Moments
Geometries
PRDDO
MNDO
VRDDO
AB INlTlO
_ _ ~
7
calculation yourself than to retrieve from nucleophile must penetrate will be intimate-
the literature a previous calculation on ly linked via the enamine pi-electron system
the same problem. to the substituent at the 3 position on the
cephem ring. We can set out to test this set
Those who are interested in the more of hypotheses using quantum mechanical
computational techniques.
pragmatic aspects of the methods just dis-
Specifically, we can use a model cephem
cussed are urged to attend one of the annual
structure with different substituents at the
workshops that are held by the Quantum
3 position; a hydroxide ion will suffice as a
Chemistry Program Exchange at Indiana
model nucleophile. The calculations will
University.’ Those workshops provide ex-
tell us about the energetics involved in the
cellent “hands-on” experience with the pop-
approach of the two reactants in this model
ular methods.
rea~tion.~ The
’ energy change can be com-
puted by the C N D 0 / 2 molecular orbital
APPLICATIONS method. C N D 0 / 2 is well suited for this
problem because it reflects quite nicely the
Having discussed some general aspects electronic effects of substituents that are
about the quantum chemical methods, at- transmitted throughout the molecule. Also,
tention will next focus on one specific area C N D 0 / 2 is relatively fast and can handle
of application. This application is note- large model structures.
worthy because of its success in illuminat- The change in energy brought about by
ing the biological activity of a significant moving the nucleophile from infinity to
class of drugs, the cephalosporin antibiotics. the optimized location near the P-lactam
The application is also of interest because ring is called the Transition State Energy
theoretical techniques provided insight into (TSE).32The more negative the TSE, the
the transition state structure of a reaction easier it is for the nucleophile to react
mechanism that is clearly pertinent to drug with the P-lactam. The TSEs range from
design.24 about - 128 to - 142 kcal/mole. The mag-
Some well known examples of cephalo- nitude does not matter. What is important
sporins are shown in Figure 2. Note that are the relative values for different substitu-
the structures differ by the substituents at ents. As the 3-substituent makes the 0-
the 3 and 7 positions on the cephem nucleus. lactam more reactive, the TSE becomes
Compared to drugs in other therapeutic more negative.
areas, much is known about the biological As seen in Figure 3, the TSEs correlate
and biochemical mode of action of ceph- with in vitro antibacterial activity against
alosporins and other 0-lactam antibi- some less resistant gram-negative patho-
o t i c ~ . ~The
. ~ availability
~-~~ of this infor- gens. The parabolic.natut-e of the curve
mation is invaluable to the application of arises because when the quantum mechan-
theoretical molecular modeling methods. ically predicted reactivity is low, then the
The P-lactam antibiotics act as acylat- compound does not acylate the bacterial
ing agents. We therefore need to examine enzymes well and the antibacterial activity
the hypothesis that the biological activity of is low. On the other hand, when the calcu-
a cephalosporin is related to the reactivity lated reactivity is too high, then the com-
of the P-lactam ring. The reactivity, in turn, pound has stability problems and decom-
may be related to how easy it is for a nucle- poses before having a chance to exert its
ophile to appr0ac.h the vicinity of the P- activity. Not many compounds have been
lactam carbonyl carbon. Furthermore, one made at the high TSE end of the scale be-
may suppose that the electron cloud above cause the compounds are difficult to obtain
and below this carbon through which the owing to their lack of stability. The opti-
Y H H
R c
- -N Tf>
0 4’
o 5 R3
COOH
Name Ri R3
0
CEPHALOTHIN -CH2- 0- C- CH3
(1964)
CEPHALEXIN -CH3
(1971)
N= N, N-N
CEFAZOLIN NbN-CH, -CH2-S Xs& C H 3
(1973)
N-N
CEFAMANDOLE -CH,-S-(
N’
“N
(1978) OH
CH3
CEFACLOR -CI
(1979)
FIGURE 2. Structures of some cephalosporin antibiotics and the year they were intro-
duced into the United States market by Eli Lilly and Company.
mum biological activity is thus achieved in biological data for a rather complex pro-
the intermediate range on the TSE scale. cess, namely, the inhibition of bacterial cell
Regression analysis can be used t o ana- growth.
lyze statistically the type of correlation seen
in Figure 3 . Irrespective of whether the
DISCUSSION AND CONCLUSION
biological activity is expressed in terms of
MICs or logarithms of the reciprocal of the In this molecular modeling study, one must
MIC, satisfactory regression equations are go beyond just looking at the three-dimen-
obtained.8.28These show that a quantum sional structure of the molecules and look
mechanically derived index is able t o ex- at the electronic properties which determine
plain more than half of the variance in the the chemical reactivity. Conversely, the
70 I I I I I I I I I I I I I
-
:
60 -
-
30
1
20
“E
0
shape of a P-lactam antibiotic structure can more electron density to shift to C(3) and
be one of the important parameters when away from C(4). The chemical shift differ-
comparing how well different 0-lactam ence correlates linearly with TSE.36 The
nuclei fit into an active Based on a second experimental observable that corre-
study of a heterogeneous set of 0-lactam lates with TSEs is the rate of alkaline hy-
antibiotics in enzyme systems of limited rel- drolysis (near pH 10) of the 0-lactam ring
evance to the lethal target enzymes, it has of 7-(thien-2-ylacetyl) cephalosporins.
been reported that goodness of fit is more 8,35.37 As one would expect, those 3-sub-
-3.1
1
-3.6
i
-w
0
-4.1
1
-4.6
CH3
-5.1 I i 1 ~ i 1 1 ~ 1 1 1 ~ 1 1
istry in the design of biologically active molecules 14. Nonbonded contacts between lone pairs on
at Lilly. Abstracts of 183rd American Chemical divalent sulfurs. J Phys Chem 1978; 82: 1407-1416.
Society National Meeting, Las Vegas, Nevada, 24. Quantum mechanics aids antibiotic design. Chem-
March 28-April 2, 1982, COMP 9. icul and Engineering News, June 16, 1980, p 27.
11. Boyd DB: Electron density and dipole moment 25. Tipper DJ and Strominger JL: Mechanism of action
analysis of valence-electron wave functions. J Am of penicillins: A proposal based on their structural
Chem SOC1972; 94: 64-70. Boyd DB: Electronic similarity to acyl-D-alanyl-D-alanine. Proc Nut1
structures of cephalosporins and penicillins. 111. Acud Sci USA 1%5; 54: 1133-1141.
EH and CND0/2D electron density maps of 7- 26. Spratt BG:The mechanism of action of penicillin.
amino-3-cephem. J Phys Chem 1974; 78: 2604- Sci Prog, Oxford, 65, 101-128 (1978).
261 1. 27. Waxman DJ, Yocum RR, and Strominger JL:
12. Halgren TA, Kleier DA, Hall JH Jr, et al: Speed Penicillins and cephalosporinsare active sitedirected
and accuracy in molecular orbital calculations: A acylating agents: Evidence in support of the sub-
comparison of CNDO/2, INDO, PRDDO, STO- strate analogue hypothesis. Phil Truns Roy Soc Ser
3G, and other methods, including AAMOM, B, London, 1980, 289: 257-271.
VRDDO, and ESE MO. J Am Chem Soc 1978; 28. Boyd DB: Theoretical studies of &lactam anti-
100: 6595-6608. biotics. Ann N Y Acud Sci 1981; 367: 531-542.
13. Dewar MJS and Ford GP: An addendum to 29. Moews PC, Knox JR, Waxman DJ, and Strom-
a recent paper by Halgren, Lipscomb, and their inger JL: Secondary structure relations between
co-workers concerning the relative accuracies of p-lactamases and penicillin-sensitive D-alanine-
several current MO methods. J A m Chem SOC carboxypeptidases. Int J Peptide Protein Res 1981;
1979; 101: 5558-5561. 17: 211-218.
14. Havlas Z and Malon P: Molecular geometries: Ac- 30. Kelly JA, Moews PC, Knox JR, et al: Penicillin
curacy test of the PCILO method. Coil Czech target enzyme and the antibiotic binding site.
Chem Commun 1980; 45: 321-329. Science 1982; 218: 479-481.
15. Zielinski TJ, Breen DL and Rein R: A MIND0/3 31. Boyd DB, Hermann RB, Presti DE and Marsh
study of some hydrogen-bonded systems. J Am MM: Electronic structures of cephalosporins and
Chem SOC1978; 100: 6266-6267. penicillins. 4. Modeling acylation by the p-lactam
16. Klopman G , Andreozzi P , Hopfinger AJ, et al: ring. J Med Chem 1975; 18: 408-417.
Hydrogen bonding in the MIND013 approxima- 32. Boyd DB, Herron DK, Lunn WHW and Spitzer
tion. J Am Chem Soc 1978; 100: 6267-6268. WA: Parabolic relationships between antibacter-
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CND0/2H and MIND0/3H. Int J Quuntum cephalosporins, penicillinate and iunsubstituted
Chem 1982; 22: 1189-1207. penems: Intrinsic reactivity and interaction with
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