The document discusses factors that determine the biological activity of phosphodiesterase inhibitors. It finds that inhibitory activity mainly depends on bond stretch energy, geometric section, number of types of molecular associates, molecule surface area, sum of atomic volumes, and sum of free carbon atomic volumes and surfaces. Inhibitory activity is influenced by the molecule's geometry and ability to complementarily fit and strongly interact with the binding site. Virtual receptor modeling shows the most active structure occupying the receptor space most completely.

1. Phosphodiesterase inhibitors:
selection of characteristics
determining biological activity
A. Knysh
V.A. Potemkin
2011
1

2. PDE4 inhibitors are used in treatment of:
• Bronchial asthma
• Chronic obstructive pulmonary disease (emphysema + chronic bronchitis)
Asthma is characterized by reversible bronchoconstriction caused by airway
hyper-responsiveness to a variety of stimuli. They include immunologic reactions
to environmental allergens, viral infections and inhaled air pollutants.
Chronic bronchitis is characterized by hypersecretion of mucus, inflammation and
decrease of airway lumen. Although the most important cause is cigarette
smoking, other air pollutants, such as sulfur dioxide and nitrogen dioxide, may
contribute.
2

3. Methylxanthines as first PDE inhibiting agents
O O CH 3
H 3C H
N H 3C N
N N
O N N N
O N
CH 3 CH 3
theophylline caffeine
• non-selective (inhibits all 5 types of PDE) • is used as a stimulating agent for
• inhibits high-polymeric fraction of PDE nervous system
whose activity is increased only during the • also inhibits PDE and adenosine
asthmatic attack receptors which is considered to be
• theophylline derivatives with higher PDE a mechanism of its stimulating effect
inhibitory activity are often proved to be • is not used for treatment of
inefficient bronchial spasmolytics bronchial asthma because of its low
• theophylline spasmolytic effect is selectivity and efficiency in
determined not only by PDE inhibitory activity comparison with theophylline
• antagonist of A1, A2 adenosine receptors • PDE inhibitory effect is reported to
• inhibits slow calcium channels show in concentrations which are
• inhibits free oxygen radical formation and behind the therapeutic corridor
releasing of inflammatory agents • stimulating effect is much more
• may cause side effects evident than that of theophylline
3

4. Mechanism of action
receptor
+ agonist PDE4 inhibitors
adenylate cyclase phosphodiesterase
ATP cAMP AMP
Ca
basophile
smooth
muscle
cell
4

5. Enzyme phosphodiesterase 4 as molecular target
• Hydrolase 3.1.4.17
• 4 chains A, B, C, D
• Zn2+, Mg2+
• Catalytic domain
Investigation of the crystal structures of the PDE4D2 catalytic domain in
complex with (R)- or (R,S)-rolipram suggests that inhibitor selectivity is
determined by the chemical nature of aminoacids and subtle
conformational changes of the binding pockets. The conformational
states of Gln369 in PDE4D2 may play a key role in inhibitor recognition.
5

6. Aims
using data on biological activity (% of in vitro inhibited enzyme),
and calculating molecular characteristics with special programs,
to find, what this activity depends on
function
?
Biological
Structure (x)
activity (y)
known
known
unknown
6

7. Training set
Basic
Benzothiadiazine Phtalasine Theophylline
structure Oxime derivatives
derivatives derivatives derivatives
(group)
OR
R O R'
R
O O H
O
R NH R N N N
N
N O
O Cl N N O
S
N
Formula O
O
N
Cl R = NHx(SO2C 6H5)2-x, R = H, COCH 3, COC6H 5
R = N(CH3)2, CO, CON(CH3)2 NHSO 2C6H4CF3/OCH3, R' = N(CH2CH 2OH)2,
R
CH2C6H 2(OCH 3)3 C(CH3)2CH2CH 2OH,
morpholine, piperidine,
R = NO2, Cl, OCH 3, OH pyrrolidine, piperazine
Number 29 12 8 14
Mean
activity 70% 23% 41% 50%
73 compounds, taken from Online Chemical Modeling Database
(www.ochem.eu Helmholtz Zentrum, Munich, Germany) 7

8. methods/programs
• HyperChem – visualization of molecules: before
calculation (using just one method of optimization, offered
by HyperChem); after calculations, including complexes
with virtual receptor, presented by set of pseudoatoms)
• MERA, MERA_MAGIC, Prok1: calculation of different
descriptors
• BiS: calculations of virtual receptor, using molecule set
in consecutive order to reconstruct the generalized self-
consistent complementary receptor for the full dataset
• STATISTICA, FieSta: mathematical processing:
correlation coefficients (>0,7; >0,5), 1,2,3 factor analysis;
regression models: graphs and equations
8

9. original data
visualization virtual receptor
after calculation
C
A
L
C
L
A
T
I
O
N statistics
visualization
before
calculation 9

10. Interpretation of results
Inhibitory activity mainly (correlation coefficients>0,7) depends on:
• bond stretch energy (‘bond’);
• geometric section (‘Ge_Sec3’);
• number of types of molecular associates (‘NC’);
• molecule surface area (‘S’);
• sum of atomic volumes (‘VOINO1R’);
• sum of free (non-overlapping) carbon atomic volumes (‘vf0ug’);
• sum of free carbon atomic surfaces (‘snefug’)
R = 0.705; inh = 0.117128*bond + 0.118559 (1 factor analysis)
R = 0.776; inh = −0.008312*Ge_Sec3 + 0.019009*NC + 0.675160 (2)
R = 0.812; inh = 0.069814*bond −0.018968*S + 0.009161*NC + 1.644785 (3)
R = 0.707; inh = −14.3722*VOIN01R + 17.6065 (1)
R = 0.818; inh = −0.078380*vf0ug + 0.588445*snefug + 0.858496 (2)
10

11. Inhibitory activity of the molecule
depends on its geometry to a
marked degree
Which is not of great wonder because
Most effective molecule - target
interactions (which usually means
the highest activity) occur with
molecules whose size let them
complementary fill the binding site
and have the strongest interactions
with the atoms at the inlet part
11

12. N
O
N
G
O
M
E
T
R
I Inhibition/bond stretch energy Inhibition/electron-electron interactions
C
F
A
C
T
O
R
S
Inhibition/number of molecular associates Inhibition/resonance
12

13. G
E
O
M
E
T
R
I Inhibition/sum of atomic volumes Inhibition/geometric section
C
F
A
C
T
O
R
S
Inhibition/sum of free carbon
Inhibition/molecule surface area atomic surfaces
13

14. Pseudoatoms of virtual receptor
The most active benzothiadiazine
structure 95%
Theophylline 26%
Pde417
Pde448
14