Molecular Modeling

Perspectives in Drug Design

Dr. Ravi Kiran Purama

Molecular Modeling
Medicinal chemists today are facing many complicated
challenges
The most demanding and perhaps the most rewarding one is the
rational design of new therapeutic agents for human diseases.
Former strategies for new drug discovery

Taking a lead structure and developing a chemical program for finding

analog molecule exhibiting the desired biological properties
Generally found by chance observation or by random screening
Later The natural ligand of the system is concerned
Involved several trial and error cycles of analysis by medicinal chemists
utilizing their experience and chemical intuition ultimately to select
chemical analog

Molecular Modeling
The entire process is laborious, expensive but conceptually
intelligent
Undeniable fact: most existing medications that are used today
from pain to fatal diseases are developed by this approach
The most advanced approaches include the efforts in
understanding the molecular processes involved in underlying
disease
Start point is to identification of the molecular target
(receptor, enzyme) in the body instead of the lead structure
Sci concept: receptors and the lock-and-key concept

Molecular Modeling
After pure protein isolation techniques & the X-ray crystallography
has come into the picture that could reveal the proteins molecular
architecture
We learn how precisely the 3-D structure regulate the life processes
Concepts of 3D- drug design:

Conceived new molecules based on similarity of the known reference

structures
On the basis of their complementarity with the 3-D structure of known
active site
molecular interactions are regulated by subtle recognition and discrimination
processes
3-D features and binding energies play an important role

Molecular Modeling
Molecular modelling is a discipline that contributes to the
understanding of these processes in a qualitative and
quantitative way
It not only analyse the molecular machinery of known system
but also the understanding of biological system functions and
predicting the prototype candidate molecules
Molecular modelling: range of computerized techniques based
on theoretical chemistry methods and experimental data to
analyse/predict molecule and molecular systems/biological
properties

Molecular Modeling
The techniques currently available provide extensive insight into
the precise molecular features that are responsible for the
regulation of biological processes: molecular geometries, atomic
and molecular electronic aspects, and hydrophobic forces.
All these structural characteristics are of primary importance in
the understanding of structure-activity relationships and in
rational drug design.
The fields important for these are molecular biology,
experimental and theoretical structural chemistry as well as
computer technologies

1st generation rational approaches in DD

RDD requires the knowledge of biological properties of molecules and
their structural features
Earlier days only the topological 2-D entities of molecules with
associated chemical and physicochemical properties
Later on Quantitative structure activity relationships (QSAR) became
popular

Based on the mathematical equations expressing biological activities in

terms of molecular parameters such as log P (the partition coefficients),
steric substituent constants (Es) and molar refractivity (MR)

This has been expanded to the use of structural indexes obtained by

quantum mechanical treatments (i.e., HOMO and LUMO energies, total
dipole moments, charge and hybridization moments, molecular
polarizability, Mulliken electronegativity, and frontier orbital indices).

1st generation rational approaches in DD

2D based QSAR approaches are conceptually relevant and not
very different from those currently used today in molecular
modeling (e.g., steric parameters, electronic indexes, hydrogen
bonding capabilities, and hydrophobicities).
Limitation: the interactions between a ligand and a protein
require much more detailed information than the ones included
in substituent indexes characterizing the molecular properties.
The second generation has shown that consideration of the full
detailed properties in 3-D is necessary in allowing the subtle
stereochemical features to be appreciated.

2nd generation rational approaches in DD

Conceptual Frame and Methodology of Molecular Modeling
molecular modeling was favoured by the fact that the
structure-activity correlations are represented by 3-D
visualizations of molecular structures and not by mathematical
equations.
looking at a drug in 3-D actually does give the impression of
knowing everything about it, including its biological properties.
molecular modeling perceives biological function
as being embedded in the 3-D structure of the molecules which
matches the point of the "lock and key" complementarity
between a drug and its biological receptor

2nd generation rational approaches in DD

Computer-aided molecular design (CAMD) is expected to
contribute to the discovery of "intelligent" molecules conceived
on the basis of precise three-dimensional stereo-chemical
considerations.
"Direct" and "indirect" designs are the two major modeling
strategies currently used in the conception of new drugs
first approach the three-dimensional features of a known receptor site
are directly considered
latter the design is based on the comparative analysis of the structural
features of known active and inactive molecules that are interpreted in
terms of their complementarity with a hypothetical receptor site model

2nd generation rational approaches in DD

Rational approaches in DD by Molecular

Modelling
The fields currently covered by Molecular modelling in
pharmaceutical research by providing tools for finding new leads
include:
Direct drug design: the three-dimensional features of the
receptor site (i.e., known X-ray structure or 3-D model of a
receptor) are directly considered for the design of lead
structures.
Indirect drug design: the analysis is based on the comparison of
the stereochemical and physicochemical features of a set of
known active/inactive molecules; lead structures are designed on
the basis of the pharmacophore model obtained by such analyses.

Rational approaches in DD by Molecular

Modelling
Database searches: lead compounds are identified from
searches using databases defined in 3-D. The input query
describes the pharmacophore; it consists of a set of molecular
fragments together with their relative location in 3-D and
additional structural constraints (geometrical or chemical).
Three-dimensional automated drug design: new lead
compounds are generated by the computer on the basis of a
"growing" procedure inside the active site of a protein whose 3D structure is known or by a computerized treatment by
assembling a set of pharmacophoric fragments defined in 3-D.

Rational approaches in DD by Molecular

Modelling
Molecular mimicry: lead molecules are conceived as mimics of
a known reference compound as, for example, the design of
mimics of selected peptide ligands.
Importance of the "Bioactive Conformation
The existence of an experimental structure for the proteinligand complex allows one to use this information to design
new molecules. The knowledge of the bioactive conformation
of the ligand as it binds to the receptor or enzyme is of great
utility in designing new mimic molecules that are potent and
specific.

Importance of the "Bioactive Conformation

The questions need to addressed in bioactive compound designing:
Experience shows that the (real) bioactive conformation of a molecule is
not necessarily the one found in solution or in the crystal.
Rather it is the specific conformation of the lowest energy in the context
of the receptor.
Knowing how the ligand is oriented in the binding pocket is also
extremely valuable in designing new structures.
The chemist tries to design a better analog of the existing prototype
structure on which he is working or a completely new chemical structure.

Rational approaches in DD by Molecular Modelling - Importance

of the "Bioactive Conformation
Typical questions include:
What are the possibilities for increasing potency?
Where can hydrophobic groups be added so that they penetrate
well into hydrophobic pockets?
Which hydrogen bond can be created between the ligand and
the protein to improve selectivity?
Where can polar groups be added in the prototype molecule
that will strengthen the binding energy of the compound?

Rational approaches in DD by Molecular Modelling - Importance

of the "Bioactive Conformation
Will this steric contact be favourable to the binding of the
molecule? Can another binding mode be considered for the
compound?
Will this side chain of the protein be able to move?
Is this modification of the prototype candidate molecule
energetically favourable for its internal energy?
Is this polar group "happy" in this subpocket?
By providing answers to such questions the molecular modeling
approach allows full utilization of the structural information
and capitalizes on what is known about the mechanism of
action of the protein-ligand complex.

MOLECULAR MIMICRY AND

STRUCTURAL SIMILARITIES
Molecular mimicry is an activity of central importance in drug
research. Very often the molecules that are created are conceived as
mimics of substances known to interact with the biological system
considered (i.e., hormones, peptides, and transmitters). For example,
peptidomimetic molecules are conceived to mimic the structure of an
endogenous peptide and are converted into a regular organic
molecule. The reason is that very often peptide molecules cannot be
developed as drugs. In general, peptide molecules are:
biologically unstable
poorly absorbed
rapidly metabolized

MOLECULAR MIMICRY AND

STRUCTURAL SIMILARITIES
A nonpeptide molecule should permit one to overcome these drawbacks.
It is expected that the synthetic molecules may provide the structural
diversity necessary to allow the molecule to be optimized for:
specificity
oral bioavailability
pharmacokinetic properties
Molecular mimicry can be considered from various points of view and
can cover many molecular properties. Actually, this is not really a new
approach in drug research; it has been inherent in most attempts aimed
at the design of drugs in a rational way. New compounds were, and
continue to be, conceived on the basis of analogies with the structures
of known active reference molecules. What has improved is the way the
molecular structures are characterized.

MOLECULAR MIMICRY AND

STRUCTURAL SIMILARITIES
Molecular modeling has become very popular because it gives access to the
very structural information necessary for the understanding of the biological
properties.
B. Structural Similarities and Superimposition Techniques
The visualization in 3-D of molecular properties (i.e., steric aspects,
electrostatic potentials, and hydrophobicity) is one step toward the
determination of similarities and differences between active and inactive
compounds.
The easiest way to reveal 3-D structural features common to a series of
compounds is the use of superimposition procedures. This technique has been
extensively used since the early seventies. For example, the analyses made
by Horn and Snyder (1971) proposing the dopamine hypothesis of neuroleptic
action provide a good illustration of this method: the X-ray structures of
chlorpromazine and dopamine are perfectly superimposable (Fig. 2).

B. Structural Similarities and Superimposition Techniques

The superimpositions are obvious when topological analogs are
considered, but they are not obvious when chemically unrelated
structures are compared. Extensive analyses were made in a variety of
therapeutic areas showing how different molecules can elicit similar
biological activities when they share common stereochemical features
in 3-D (see Chapter 3 and references cited therein). This has led to the
development of 3-D pharmacophoric models that are necessary for the
rational design of new lead compounds.
The structures are usually aligned on the basis of their atomic
positions, but very often the alignment can be very subjective. The
best way to reduce subjectivity is to compare the molecules in 3-D in
the actual space of their physicochemical properties [sometimes
designated as four-dimensional (4-D) representations] (Fig. 3).

As far as computerized superimposition techniques are concerned, this perspective is relatively new. New
developments in this field are in progress and should provide a powerful means for obtaining good structural
pharmacophore models.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
A. An Important Key and the Role of the Molecular Modelist
In pharmaceutical research the fundamental aspiration is to
convert knowledge, intelligence, and imagination into practical
results.
In this multidisciplinary process the molecular modelist has
become an important element.
Molecular modeling in the past was not always accepted by the
traditional medicinal chemist. It was very often considered an
unproven and less efficient approach than those that were
currently in use.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
It is desirable to replace whenever possible the expression
"rational" by terms such as "structure-based," "mechanismbased, .... direct," or "indirect drug design.
The combination of "intuition" and "rational aspects are
actually the very driving force of any modern scientific
innovation.
In drug design, chemical intuition is an important element
because in this field one has to be willing to make predictions
based on incomplete information and models (Snyder, 1991).

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
B. Limitations of Chemical Intuition
Progress in structural chemistry and in molecular modeling has
considerably contributed to improve the perception of the chemists
by expanding their current chemical intuition.
Chemical intuition is a good complement and develops together
with knowledge. Chemical intuition and knowledge both expand
continuously and each one redefines new limits to the other.
The interactions occurring in this process constitute the dynamics
of creation in research. One example is presented here to illustrate
some of their relationships along with some of their limits.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
The example concerns the inhibition of cytochrome P450
This class of enzymes is a widely occurring class of heme
proteins that catalyze the hydroxylation of aliphatic and
aromatic molecules.
Camphor is the natural substrate of the bacterial cytochrome
P450cam and is stereospecifically hydroxylated in the 5-exo
position
It was found that phenylimidazoles, such as phenyl-1,
phenyl-2, or phenyl-4, inhibit this hydroxylation process

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION

Rational: From the structural point of view

it seems reasonable to assume that the
three inhibitors bind to the enzyme
in a way where all the phenyl rings are
aligned

FIGURE 5 Looking for 3-D features common to

Phenylimidazoles: superimposition of phenyl
rings

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
This superimposition has the advantage of showing that the three
molecules have almost identical shapes and can therefore occupy the
same hypothetical subpocket in the enzyme catalytic site. This should
correspond to the true solution if the binding is driven by
consideration of the geometrical features.
If this is not the case and if, in particular, the electronic aspects play
an important role, the model considered should be discarded because
it does not distinguish between nitrogen and carbon atoms in the
superimposition of the molecules.
In an alternative solution satisfying the alignment of electronic
features, one should consider superimposing the molecules in such a
way that the nitrogen atoms are optimally superimposed.

V. RATIONAL DRUG DESIGN AND CHEMICAL INTUITION

FIGURE 6 Looking for common 3-D features to
Phenylimidazoles: superimposition of phenyl
rings

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
The new solution is far from being perfect: the 3-D diversity of
the positions occupied by the phenyl rings does not provide
convincing evidence of the validity of such a possibility.
At this point the important question is what are the
determinant factors ?
Are they steric, electronic, or are both involved?
In the absence of additional information for discriminating
between the two alternative models, one would perhaps tend
to favor, in the first place, the steric model of Fig. 5.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
The correct answer is actually known: the X-ray structures of the
complexes with the substrate camphor and with the three
phenylimidazole inhibitors with cytochrome P450cam from
Pseudomonas putida have been resolved (Poulos et al., 1987; Poulos
and Howard, 1987).
Therefore one can look at the exact binding modes observed for the
different ligands. The camphor molecule binds with a strong hydrogen
bond to the hydroxyl group of a Tyr-96 residue of the heme protein
(Fig. 7).
This explains why, in the natural pathway, the 5-exo position is
stereospecifically hydroxylated, being located just on top of the heme
iron.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION

FIGURE 7 Binding mode of Camphor in the

catalytic site of cytochrome p450cam

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION

FIGURE 8 Binding of phenyl-2-imidazole with

cytochrome p450cam

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
It is interesting to see how the different phenylimidazoles bind to the
protein. The first complex with phenyl-2-imidazole shows a situation
where the imidazole ring is anchored to the protein via the Tyr-96
residue already mentioned earlier, with the phenyl fragment pointing
toward the heme (Fig. 8).
In the case of the phenyl-1- and phenyl-4-imidazoles, the situation is
very different. A chelation is observed between the iron of the heme
and a nitrogen atom of the imidazole ring (Fig. 9).
It becomes possible to visualize the superimposition of the three
molecules in their observed binding modes. Figure 10 shows clearly
that the correct answer to the question posed earlier corresponds to a
situation where neither the phenyl groups nor the imidazoles are
aligned.

FIGURE 9 Binding modes of phenyl-1- (a) and phenyl-4- (b)

imidazoles with cytochromeP450cam.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
Useful achievements have been made in this project; in particular, very
potent inhibitors have been designed showing a double anchorage to both the
iron of the heme and the tyrosine residue.
This example illustrates that although chemical intuition has often proven to
be very useful in compensating for the lack of knowledge, there are situations
where a minimum of indispensable data is necessary, in the absence of which
the reality is masked and an approach could be counterproductive.
In the example discussed earlier, the knowledge that the biological activities
of the compounds involve the binding with a heme protein is of high
informational content.
From this information one could already exclude the possibility of a common
binding mode for the three ligands: whereas in phenyl-1- and phenyl-2imidazole the substitution patterns allow a complexation of the heme group
by the imidazole moiety, this is impossible in the phenyl-2 congener due to a
steric clash between the phenyl and the porphyrin rings.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION

FIGURE 10 Binding of phenyl-2-imidazole with

cytochrome p450cam their common structural
features

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
This example suggests the following:
optimal conditions for direct molecular modeling consist of
having some knowledge about the macromolecular target or,
even better, an X-ray structure of a complex between a ligand
and the protein.
in indirect modeling, good models can be derived through the
design of appropriate experiments to resolve the observed
contradictions.
optimal conditions in a project exist when working hypotheses
and experimental undertakings are combined.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
The field of molecular modeling has advanced since the 1980s.
The achievements made in computer technology, theoretical structural chemistry,
biotechnology, protein crystallography, and high field NMR have permitted the development
of molecular modeling.
The visualization of complex threedimensional structures with their associated properties
such as geometries, electrostatic, and hydrophobicity provide useful means in understanding
some of the driving forces operating in life processes.
Such information allows one to rationalize structure-activity relationships and has proven to
reduce the role of empiricism in the design of new prototype drugs.
It is probably just an aesthetic hope to envisage that a new drug will be the pure result of
this approach. Nevertheless, it is now evident that the technique has already contributed to
the realization of outstanding achievements in a number of research programs.
It is rare that the announcement of the development of new drugs obtained through such
rationales are published in mainstream international financial journals, but examples exist,
such as the announcement in the The Wall Street Journal (issue of January 1994) of the
development of a new class of AIDS drugs by the DuPont Merck Pharmaceutical Co.; others
will certainly follow.

V. RATIONAL DRUG DESIGN AND

CHEMICAL INTUITION
As far as methodology is concerned, the limitation that currently exists concerns, in
the first place, the calculation of the free energy of binding of ligands to a protein
enzyme or receptor.
The exact calculation of this quantity is crucial for structure-based drug design
because the interaction of the ligand with the macromolecular protein (which
eventually leads to inhibition of the enzyme or antagonism of the receptor) is
generally directly related to these energies.
When it is possible to perform this calculation in a reliable manner, direct drug
design will require much less iteration in the discovery cycle and will significantly
shorten the drug development cycle.
However, new progress in this direction requires taking into consideration complex
desolvation and solvation processes that occur during the binding process.
New advances in this area will occur only if substantial breakthroughs are also made
in computer technology in order to have acceptable computing times for such
treatments.