Vol.2, No.7, 661-671 (2010)
Copyright © 2010 SciRes. Openly accessible at http://www.scirp.org/jo urna l/HEALTH/
Computer-assisted anti-AIDS drug development:
cyclophilin B against the HIV-1 subtype A V3 loop
Alexander M. Andrianov1*, Ivan V. Anishchenko2
1Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus;
*Corresponding Author: andrianov@iboch.bas-net.by
2United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Belarus
Received 16 December 2009; revised 24 March 2010; accepted 26 March 2010.
Aim: The objects of this study originated from
the experimental observations, whereby the HIV
-1 gp120 V3 loop is a high-affinity ligand for
immunophilins, and consisted in generating the
structural complex of cyclophilin (Cyc) B be-
longing to immunophilins family with the virus
subtype A V3 loop (SA-V3 loop) as well as in
specifying the Cyc B segment forming the
binding site for V3 synthetic copy of which, on
the assumption of keeping the 3D peptide struc -
ture in the free state, may present a forward-
looking basic structure for anti-AIDS drug de-
velopment. Methods: To reach the objects of
view , molec ular docking of the HIV-1 SA-V3 loop
structure determined previously with the X-ray
conformation of Cyc B was put into practice by
Hex 4.5 program (http://www.loria.fr/~ritchied/
hex/) and the immunophilin stretch responsible
for binding to V3 (Cyc B peptide) was identified
followed by examination of its 3D structure and
dynamic behavior in the unbound status. To
design the Cyc B peptide, the X-ray conforma-
tion for the identical site of the native protein
was involved in the calculations as a starting
model to find its best energy structural variant.
The search for this most preferable structure
was carried out by consecutive use of the mo-
lecular mechanics and simulated annealing
methods. The molecular dynamics computa-
tions were implemented for the Cyc B peptide
by the GROMACS computer package (http://
www.gromacs.org/). Results: The overmolecular
structure of Cyc B with V3 was built by com-
puter modeling tools and the immunophilin-
derived peptide able to mask effectively the
structurally invariant V3 segments embracing
the functionally crucial amino acids of the HIV-1
gp120 envelope protein was constructed and
analyzed. Conclusions: Starting from the joint
analysis of the results derived w ith those of the
literature, the generated peptide was suggested
to offer a promising basic structure for making a
reality of the protein engineering projects aimed
at developing the anti-AIDS drugs able to stop
the HIV’s spread.
Keywords: HIV-1; V3 Loop; Cyclophilin B;
Computer Modeling; Molecular Docking;
Anti-Aids Dru g Design
The HIV-1 envelope glycoprotein (Env), the etiologic
agent of AIDS [1], consists of two noncovalently bound
subunits derived from the gp160 precursor. One of these
subunits, gp120 protein, is localized on the surface of the
viral isolates and becomes a direct party to the virus
binding to the target-cells, whereas the other, trans-
membrane gp41 protein, triggers the process of mem-
brane fusion resulting in the invasion of the virus ge-
nome into the macrophages and T-lymphocytes [2]. Spe-
cific interactions of the HIV-1 with the virus primary
receptor CD4 as well as with its chemokine co-receptors
CCR5 and/or CXCR4 are put into effect using the
V1-V5 loops of gp120 disclosing the high variability of
the amino acid sequences in diverse virus strains [3-5].
Currently, special emphasis of the research teams in-
volved in the anti-AIDS drug studies is attracted to the
HIV-1 V3 loop (reviewed in [6]). The higher interest in
V3 is caused by numerous experimental data [7] testify-
ing to the fact that exactly this gp120 site gives rise to
the principal target for neutralizing antibodies and ac-
counts for the choice of co-receptor determining the
preference of the virus in respect with T-lymphocytes or
primary macrophages [8]. The differential usage of co-
A. M. Andrianov et al. / HEALTH 2 (2010) 661-671
Copyright © 2010 SciRes. Openly accessible at http://www. scirp.org/journal/HEALTH/
receptors, which is critically dependent on the sequence,
charge, and/or structure of the V3 region of gp120 [9,10],
dictates the viral phenotype, which shows a typical pat-
tern of evolution during the natural history of HIV-1
infection. CCR5-restricted strains (R5) are the most
prevalent in vivo, as they are almost invariably response-
ble for the initial transmission, predominate during the
long asymptomatic phase of the infection, and often per-
sist after the progression to full-blown AIDS; by contrast,
strains that utilize CXCR4, either alone (X4) or in com-
bination with CCR5 (R5X4), emerge only in a subset of
patients, typically in conjunction with the onset of clini-
cal signs of disease progression and immune system
deterioration [11,12].
Since the V3 loop governs the cell tropism and cell
fusion [7], one of the strategic ways in developing the
anti-HIV-1 drugs may be based on the approach antici-
pating the search for the chemicals able to block effi-
ciently this functionally significant stretch of gp120 [6].
Comprehensive analysis of the data given in study [13]
allows one to suppose that immunophilins exhibiting
specific high-affinity interactions with the HIV-1 V3
loop may be utilized as a basic substance to set out of the
search for the potential anti-AIDS therapeutic agents.
Immunophilins known originally as the cellular re-
ceptors of the immunosuppressive drugs cyclosporine A
and FK506 or rapamycin organize the extensive group of
proteins exhibiting peptidyl-prolyl cis-trans isomerase
activity which is inhibited specifically and efficiently on
binding of the corresponding immunosuppressant [14].
Immunophilins subdivided into three families of proteins,
namely cyclophilins and FK506-binding proteins (FK
BPS), and a novel chimeric dual-family immunophilin,
named FK506- and Cyclosporine-binding protein
(FCBP) show similar enzymatic and biological functions
despite the apparent difference in their sequence and
three-dimensional structures [15]. Alongside with the
function of intracellular receptors of immunosuppres-
sants, individual representatives of immunophilins act as
catalysts of protein folding and as shaperones stabilizing
proteins in a defined conformation and supervising the
quality of their spatial structure [16,17]. A variety of
bacterial and protozoan pathogens express FKBP-related
peptidyl- prolyl cis-trans isomerases termed macro-
phage-infectivity potentiators (Mip). Mip proteins act in
host cell infection as virulence factors, either as mem-
brane-bound proteins on the surface of the pathogens or
as soluble secreted proteins [18,19]. The peptidyl-prolyl
cys-trans isomerase activity of Mip proteins is sup-
pressed by FK506, which reduces the infectivity of the
pathogens without affecting the rate of intracellular rep-
lication. Distinct immunophilins were found to be re-
leased from cells. Cyclophilin B was detected in human
milk [20] and blood plasma [21], but is mainly localized
in the endoplasmatic reticulum of cells. The cytosolic
immunophilins cyclophin A and FKBP12 were shown to
be released during apoptosis of fibroblasts [22] and to
act as chemokines by unknown mechanism [23-25]. Re-
cent researches have revealed that many immunophilins
possess a shaperone function independent of pepti-
dyl-prolyl cis-trans isomerase activity (reviewed in [15]).
Knockout animal studies have confirmed multiple essen-
tial roles of immunophilins in physiology and develop-
ment consisting in interactions with proteins to guide
their proper folding and assembly [15].
Reasoning from the empirical observations, there is a
good motive to think that immunophilins present in
normal human blood plasma are directly relevant to the
HIV-1 replication assisting the virus with getting into
macrophages and T-lymphocytes [26]. In particular, cy-
clophilin A packaged into nascent virus particles by spe-
cific binding to the capsid region of the Gag precursor
protein at the time of viral assembly [27-29], was found
to mediate the HIV-1 attachment to the target cells via
heparans followed by the gp120-CD4 interaction [26].
Due to the interaction of immunophilins with the HIV-1
isolates, their role of conformases or docking mediators
in the virus life cycle seems to be highly probable, since
immunophilin receptors on cell membranes and im-
munophilin-related virulence factors of pathogens have
been identified [13].
This work proceeds with our previous studies [30,31]
where two virtual molecules, namely FKBP and Cyc A
peptides, presenting the promising anti-HIV-1 pharma-
cological substances were designed by means of com-
puter modeling based on the analysis of specific interac-
tions of the FK506-binding protein and cyclophilin A
with V3.
The object of the present study was to model the
structural complex of one more protein from immuno-
philins superfamily, cyclophilin (Cyc) B, with the HIV-1
subtype A V3 loop (SA-V3 loop) circulating in Eastern
Europe including Republic of Belarus and, therefore,
offering the target of our special interest, as well as to
specify the Cyc B segment forming the binding site for
V3, the synthetic copy of which, on the assumption of
keeping the 3D peptide structure in the free state, may be
considered as a forward-looking applicant for the role of
a new antiviral drug.
To this effect, molecular docking of the HIV-1 SA-V3
structure determined previously [32] with the X-ray
conformation of Cyc B was put into practice, and the
Cyc B stretch responsible for the binding to V3 was
identified followed by predicting the most probable 3D
structure of this stretch in the unbound state, studying its
dynamic behavior, and collating the results obtained
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with the X-ray data for the corresponding site of Cyc B.
Thereupon, the potential energy function was analyzed
for the complex of the SA-V3 loop with the Cyc B pep-
tide offering the virtual molecule that imitates the Cyc B
segment making a key contribution to the interactions of
the native protein with V3. As a matter of record, the
designed peptide was shown to be capable of the effect-
tive masking of the functionally critical and structurally
rigid V3 sites, presenting the suitable framework for
making a reality of the protein engineering projects util-
izing the V3 target for developing the anti-AIDS drugs
able to stop the HIV’s spread.
2.1. Molecular Docking Simulations
Molecular docking of the SA-V3 loop [32] with Cyc B
(file 1CYN of the Protein Data Bank [33,34]) as well as
with the Cyc B peptide was executed by the Hex 4.5
program [35] which presents an interactive molecular
graphics package for calculating and displaying feasible
docking modes of pairs of protein and DNA molecules
and employs the spherical polar Fourier correlations to
accelerate the computations. Energy refinement of the
generated complexes was performed in the GROMACS
package [36] by minimizing their potential energy. To
this end, the conjugate gradient method was used for the
complex of the native protein with the V3 loop as well
as for the overmolecular ensemble of V3 with the Cyc B
peptide. At the final point of computations, the structural
complexes were subjected to the procedure of simulating
annealing carried out during 100 ps time domain at ini-
tial and final temperatures equal to 500 and 0 K respect-
2.2. Determination of the 3D Static Structure
for the Cyc B Peptide and Molecular
Dynamics Computations
To design the 3D structure of the Cyc B peptide, the
X-ray conformation of the Cyc B site [37] responsible
for its binding to V3 was involved in the calculations as
a starting model to find its best energy structural variant
in the unbound form. The search for this most preferable
conformation was executed by consecutive use of the
molecular mechanics and simulated annealing methods
realized in the Tinker package [38] with activating its
program modules Minimize and Anneal.
The molecular dynamics (MD) simulations of the
built Cyc B peptide structure were implemented by the
GROMACS computer package [36] using the GRO-
MOS96 force field parameter set 53A6 [39]. The starting
3D structure of the CycB peptide generated hereinbefore
was placed in a cubic box so that the smallest distance
between its walls and the peptide atoms was greater than
the half of the cut-off radius of the Coulomb and Len-
nard-Jones potentials fixed at 1.4 nm. Simple point
charge water model [40] was utilized to set the parame-
ters of explicit solvent on which the periodic boundary
conditions were imposed in all directions. Before the
MD computations, the initial Cyc B peptide model was
subjected to the procedure of energy minimization real-
ized in vacuum by the steepest descent method. The MD
simulations were carried out at temperature 310 K dur-
ing 20.5 ns time domain with 1 fs step at fixed pressure
and number of atoms, the first 0.5 ns being the stage of
solvent relaxation. To integrate the Newton’s equations
of motion, the common leap-frog algorithm was used. To
control the temperature, the weak coupling scheme to an
external bath [41] was employed in the calculations with
0.1 ps characteristic time. As with the temperature cou-
pling, the system was linked to a “pressure bath” by ex-
ponential relaxation of pressure [41] with 1.0 ps time
Every 10 ps, the geometric parameters of the MD
structures and the data on their energy characteristics
were recorded into the trajectory file. Comparison of the
MD conformations between themselves and with the
input structure was performed in terms of the values of
root-mean-square deviations computed both in Cartesian
and angular space. To this effect, the GROMACS rou-
tines [36] were implicated in the studies.
The computations were run in parallel on SKIF K-1000
computer cluster on 64 CPUs [42].
2.3. Identification of Secondary Structures
in the Cyc B Peptide
To determine the different types of secondary structures
in the Cyc B peptide, the , ψ values for all of the
amino acids derived from the simulated model were
analyzed in compliance with the criteria given in study
[43]. The types of β- and -turns were identified within
the classification of Hutchinson and Thornton [44]. To
detect the nonstandard β-turns, the additional informa-
tion on the distances Cαi…Cαi+3 computed from the atomic
coordinates of the simulated structures was employed.
2.4. Collation of 3D Static Structures
The values of root-mean-square deviations (RMSD) in
atomic coordina tes (cRMSD) were taken to evaluate the
similarity of the structures in the Cartesian space [45].
To compare the structures in terms of the dihedrals, the
RMSD between corresponding angles (aRMSD) were
used as a measure of their conformational similarity in the
angular space [45].
A. M. Andrianov et al. / HEALTH 2 (2010) 661-671
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3. RESULTS AND DIS CUSSION Gly-17, Gln-18, Ala-19, Thr-23, and Arg-31 take up po-
sitions nearby the surface of Cyc B giving rise to the
binding site for V3 by means of Gly-1, Pro-2, Lys-3,
Gly-28, Lys-29, Thr-30, Lys-91, Lys-93, and Glu-178.
One needs to note that cooperation of the V3 loop with
Cyc B results in the origin of one ion pair organized by
Arg-31 of V3 and Glu-178 of Cyc B and in the formation
of six H-bonds that appear as a result of donor-acceptor
interactions of the receptor amino acids Lys-91, Lys-93,
and Glu-178 on the one hand as well as of V3 residues
Ser-11, Val-12, Gln-18, Ala-19, and Thr-23 on the other
hand (see information given in Table 1).
Figure 1 casts light on the structural complex of the
HIV-1 SA-V3 loop with Cyc B generated via molecular
docking of their 3D structures followed by optimization
of its geometric parameters. Insight into the function
describing the energy surface of the built complex makes
it clear that the binding of V3 to Cyc B initiates the for-
mation of stable overmolecular structure that is charac-
terized by the value of potential energy equal to 6434
kcal/mol. Analysis of the matrix of interatomic contacts
coming true in the designed complex allows one to iden-
tify the amino acids of V3 and Cyc B participating in the
intermolecular interactions the total energy of which
comes to 75 kcal/mol. So, according to the data obtained,
such V3 residues as Ser-11, Val-12, Gly-15, Pro-16,
These results signify that interaction of the V3 loop
with Cyc B entails the blockade of its central region
making the immunogenic crown of gp120 [46], whereas
the residues of V3 N- and C-terminal segments (except
Figure 1. Image of the structural complex between the HIV-1 SA-V3 loop (tubes) and Cyc B (balls).
Table 1. Geometric parameters of intermolecular H-bonds for the structural complex of the HIV-1 SA-V3 loop with Cyc B.
Distance (Å)
Distance (Å)
Lys-932 NH Gln-181 OE1 2.7 1.7
Lys-932 NZ Thr-231 OG1 2.8 1.8
Ser-111 OG Glu-1782 OE2 2.7 1.7
Gln-181 NH Lys-912 CO 2.8 1.9
Gln-181 NE2 Glu-1782 OE2 2.8 1.9
Ala-191 NH Lys-912 CO 3.0 2.0
Footnote: Superscripts 1 and 2 denote the amino acids of V3 and Cyc B respectively.
Openly accessible at
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for Arg-31) relating to its stem [46] do not come in direct
contact with the receptor. The data above are in harmony
with those of study [13], whereby high affinity to im-
munophilins is typical not merely for intact V3 variable
loops but also for their peptides embracing the immuno-
genic tip of gp120. Among the segments of V3 interact-
ing effectively with Cyc B, it is essential to mark its
tripeptide Gly-15-Pro-16-Gly-17 occurring actually in
all of the deciphered amino acid sequences of the HIV-1
principal neutralizing determinant [47]. Functional role
of this invariant V3 stretch has not been completely
specified. Nevertheless, it as known that, even a single
substitution for its central residue by alanine makes an
impact both on the virus immunogenicity and infectivity
[48] testifying to important role of Pro-16 in the HIV-1
life cycle. Under the data derived, the 3D structure of the
V3 fragment of interest is practically identical to that of
Cyc B site Gly-1-Pro-2-Lys-3 which is spatially close to
it: the value of cRMSD computed for all of the atoms of
their main chains totals 0.7 Å. Resem- blance of the 3D
main chain shapes observed for the two segments of the
ligand and the receptor makes it possible to suggest that
Cyc B stretch Gly-1-Pro-2-Lys-3 gives rise to the signal
structure that is interpreted by V3 as a mirror image of
its own immunogenic crest, which, most likely, presents
the head reason involving the specificity of V3 interac-
tions with immunophilins. In this light, the findings
above confirm the validity of the assumption made in
our previous studies [30,31] where specific high-affinity
interactions of the HIV-1 V3 variable loops with im-
munophilins arising from experimental observa- tions
[13] were suggested to be stipulated by appearing in
their amino acid sequences the fragments exposing the
similar 3D structures which are constructed from -turns
of polypeptide chain (for details see works [30,31]).
In such a way, the data of molecular docking testify to
realizing the energetically favorable contacts of the HIV-1
SA-V3 loop with Cyc B resulting in the masking of
some of the key V3 amino acids of its immunogenic
crown. In this context, we could suggest of a possible
usage of immunophilins and, in particular, Cyc B as an
alternative to the V3-directed antibodies commonly used
to neutralize the HIV-1 activity. However, the evidence
of study [49] demonstrating that increase of immuno-
philins concentration in infected blood plasma does not
influence the virus infectivity conflicts with this primi-
tive conjecture. In the case of Cyc B, the probable cause
of its insufficient neutralizing activity may consist in the
fact that, as follows from our simulations, the binding of
the immunophilin to the HIV-1 V3 loop occurs via in-
teractions with the central region of V3 and does not
affect its N- and C-terminals (Figure 1) where the major
portion of the residues involved in cell tropism and cell
fusion is localized [50-52]. Therefore, to amplify the
blockade of V3 and preserve its capacity for specific
interactions with Cyc B, we have undertaken an attempt
to design as potential anti-HIV-1 drug the virtual mole-
cule named Cyc B peptide and imitating N-terminal
segment 1-30 of the native immunophilin. The choice of
Cyc B segment 1-30 for continuation of our studies is
caused by the following motive: in compliance with the
designed data, it holds tripeptide Gly-1-Pro-2-Lys-3
recognizable by the virus immunogenic crest and com-
prises significant share of the residues making the bind-
ing site for V3. Certainly, such a definition is correct
only in case that the 3D structure of this Cyc B segment
does not experience the considerable alterations in its
free state. To check whether that is true, we computed
the most preferable 3D structure of the Cyc B peptide
and compared it with the one appearing in crystal [37] in
the corresponding site of the intact protein. Analysis of
Figure 2 illustrating the image of the superposed peptide
structures gives grounds to conclude that the spatial
folds of their backbone are closely related, and this in-
ference arising from visual observation is ratified by the
value of cRMSD equal to 2.4 Å. At collating the struc-
tures given in Figure 2, it is essential to underscore that
very close agreement between them (cRMSD is 0.5 Å)
occurs in segment Gly-1-Pro-2-Lys-3 that, as stated
above, forms in the native Cyc B the conformational
epitope specifically recognizable by V3. Analogous con-
clusion to the effect that the compared structures are
alike follows from their confrontation in the conforma-
tional space (, ): the value of aRMSD calculated for
all of the peptide amino acids comes to 33.
Insight into the static model for the 3D structure of the
Cyc B peptide (Figure 3(a)) shows that essential con-
tribution to its energy stabilization belongs to the donor-
acceptor interactions that result in forming the extensive
network of hydrogen bonds appearing between amino
acids both distant and adjacent in the polypeptide chain.
The molecule generated by computer modeling tools
offers the elongated “construction” in which the spatially
close N- and C-terminal residues give rise to the long-
range H-bond by the oxygen of Gly-1 carboxyl group
and the hydrogen of hydroxyl group of Thr-30 side chain.
As follows from the dihedral values given in Table 2,
central part 10-22 of the Cyc B peptide constitutes the
-sheet the “oval isthmus” of which is composed from
consecutive -turns (Figure 3(b)), with their spatial
folds being similar to those previously [32] in the imm-
unogenic crown of the HIV-1 SA-V3 loop. In particular,
according to our simulations, tetrapeptide Ile-14-Gly-15-
Asp-16-Glu-17 of the Cyc B peptide adopts the confor-
mation of none-standard -turn IV close to that of stretch
Gly-15-Pro-16-Gly-17-Gln-18 of V3: in this case, the
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Table 2. Dihedral angles for amino acids in the 3D structure of
the Cyc B peptide.
Dihedral angles (deg.)
ψ χ1 χ2 χ3
Gly-1 — –109.7 — — —
Pro-2 –52.2 178.6 –18.1 31.0
Lys-3 –135.3 170.1 –64.6 –176.2 –69.6
Val-4 –84.6 141.8 176.6 — —
Thr-5 –135.9 –136.8 69.1 — —
Val-6 –60.6 123.4 –62.0 — —
Lys-7 –93.7 80.2 –173.1 59.0 168.0
Val-8 –112.5 160.8 –153.8 — —
Tyr-9 –78.7 170.2 78.2 –82.8 —
Phe-10 –144.3 161.7 –168.0 –101.0 —
Asp-11 –85.7 165.1 –141.6 –58.4 —
Leu-12 –147.4 101.0 –154.5 –50.8 —
Arg-13 –129.4 102.0 –45.8 –162.4 70.9
Ile-14 –80.3 88.7 –55.0 –179.9 —
Gly-15 74.1 –72.1 — — —
Asp-16 –147.8 5.8 –152.3 –61.9 —
Glu-17 –53.7 120.6 –64.8 –176.4 –30.7
Asp-18 –74.2 42.0 –157.7 –137.1 —
Val-19 –52.9 –31.1 –165.5 — —
Gly-20 118.2 –175.8 — — —
Arg-21 –80.9 55.8 –75.7 157.4 –70.7
Val-22 –53.2 129.0 179.8 — —
Ile-23 –76.6 60.7 –39.7 –59.3 —
Phe-24 –56.9 –63.3 –66.1 –75.9 —
Gly-25 77.9 171.0 — — —
Leu-26 –138.0 159.7 –66.5 95.1 —
Phe-27 –97.0 –5.3 –51.8 –83.5 —
Gly-28 61.7 –130.8 — — —
Lys-29 –133.8 143.2 176.9 63.7 169.4
Thr-30 –122.6 — –62.2 — —
Figure 2. 3D structure of the Cyc B peptide superposed with
the X-ray conformation for segment 1-30 of the entire protein.
Figure 3. (a) Three-dimensional; (b) structures of the Cyc B
peptide generated based on the X-ray conformation of site 1-30
for the intact Cyc B.
value of cRMSD estimated for the backbone atoms of the
compared structures is 1.1 Å. Resemblance in the struc-
tural organization of the central regions of V3 and the
Cyc B peptide takes also place for their longer fragments.
For instance, if we compare the 3D structure of V3
stretch 15-20 producing the overwhelming majority of
contacts with neutralizing antibodies (study [53]) with
the one of the Cyc B peptide segment 14-19, it is also
possible to observe the conformity of their spa- tial
backbone folds (the corresponding value of cRMSD
aggregates 2.0 Å). This outcome enables one to assume
that, subject to the observance of the principle of “mirror
similarity” formulated in studies [30,31], segment of the
Cyc B peptide forming the “oval isthmus” of the -sheet
and located in the native protein inside its globule may
give an additional site for specific binding to V3 alterna-
tive to stretch Gly-1-Pro-2-Lys-3 of the intact immuno-
When looking into the secondary structure of the de-
signed molecule (Figure 3(b)), one cannot but catch
sight of the peptide segment 27-30 that, as the stretches
A. M. Andrianov et al. / HEALTH 2 (2010) 661-671
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of its central part, exposes the conformation of -turn,
which merits the principal concern in view of the data on
the 3D structure of the SA-V3 loop [32] where the
C-terminal site organizes exactly the same structural motif.
This evidence combined with that above implicates the
following conclusion: the secondary structures of V3 and
the Cyc B peptide observed in their central and C-termi-
nal portions are closely related. In addition, considering
the main chain dihedrals (Table 2) indicates that, except
-turns, the analyzed structure also forms -bends the
central residues of which are located in positions 15, 18,
and 21 (Figure 3(b)).
The results of molecular dynamics simulations im-
plemented during 20 ns time domain by applying the
static 3D structure of the Cyc B peptide as the starting
model are evidence of its relative conformational rigidity:
the average of cRMSD calculated for the structures of
the MD trajectory and starting point amounts 3.1 Å and
the system of intramolecular H-bonds serving as one of
the factors stabilizing the molecule structure undergoes
no drastic changes within the whole MD trajectory.
Nonetheless, comprehensive study on the dynamic struc-
tures of Cyc B peptide indicates that their individual rep-
resentatives differ significantly from the input structure,
which does not exclude the probability of wide-ranging
structural reorganizations of this molecule stimulated by
abrupt alterations of the environment that, for example,
may happen upon its entry into numerous intermolecular
Conformity of the 3D structure of the Cyc B peptide
with that of the same immunophilin segment (Figure 2)
and its relative structural inflexibility following from the
data of molecular dynamics computations give ground to
believe that the molecule designed here may not only
conserve the capacity for specific interaction with V3
characteristic of the native protein [13] but also intensify
the blockade of this cryptic site of gp120. Indeed, delv-
ing into the potential energy function describing the
structural complex of the Cyc B peptide with V3 illus-
trates (Figure 4) that, as compared to the native protein,
the peptide originating from its framework exhibits
much more extensive network of contacts with the V3
segments embracing the biologically significant amino
acids of gp120. So the energy of intermolecular interact-
tions in the complex of Cyc B with V3 amounts to 75
kcal/mol and, in the case of interest, its value falls down
to 350 kcal/mol. And at the same time, stabilization of
the complex between the Cyc B peptide and V3 is
reached owing to the multiple donor-acceptor interac-
tions (see Table 3 ) as well as to the salt bridge formed
using Arg13 of V3 and Asp-18 of immunophilin-derived
peptide. When analyzing the system of H-bonds given in
Ta bl e 3, there is need to note that, from the side of V3,
contribution to its formation belongs to such biologically
meaningful residues of gp120 as Lys-10, Arg-13, Gly-17,
Gln-18, Asp-25, Asp-29, Ile-30, and Arg-31 which find
themselves to be isolated as a result of arising the over-
molecular ensemble. Among the residues of this regis-
ter, we ought to notice Asp-25 that takes an active part in
binding of the virus to the cell membrane surface [54-58]
and, along with Ser-11, accounts for the HIV-1 pheno-
type [59,60]. Constituting the complex of the Cyc B pep-
tide with V3 also entails the masking of its functionally
critical amino acids Ser-11, Ala-19, Ile-23, Gly-24, and
Gln-32 which are also utilized by the virus to set up the
cell tropism determinant [54-58]. The active center of
V3 responsible for binding to Cyc B peptide contains
Asn-6 the blockade of which may be highly effective for
the virus inactivation: as mentioned above, this amino
acid of V3 presenting the integral part of its structurally
invariant segment 3-7 [32] gives rise to one of the con-
served sites of N-linked glycosylation of gp120 [61].
When examining the overmolecular ensemble repre-
sented in Figure 4, one needs to cast a glance at the fol-
lowing feature: in this complex, segment Gly-1-Pro-2-
Lys-3 of the Cyc B peptide interacts with structurally
rigid stretch 28-32 of the HIV-1 V3 domain [32], whereas
the corresponding site of the native protein, as stated
before, contacts the immunogenic crown of gp120 (Fig-
ure 1). At the same time, this V3 region that proves to be
unused by the N-terminal site of the Cyc B peptide be-
comes very intimate with pentapeptide Ile-14-Gly-15-
Asp-16-Glu-17-Asp-18 belonging to the “oval isthmus”
of its -sheet. These observations are of special interest
since the indicated segments of the receptor and ligand
reside in the -turns of polypeptide chain which may
serve as docking sites for protein-protein interactions
[62-64]. The presence of -turns in the 3D structures of
V3 and the Cyc B peptide is likely to be one of the head
factors that may make a determinative contribution to
the specificity of their efficacious interactions.
Collating the 3D structures of V3 and the Cyc B pep-
tide in natural and constrained states indicates that, in
either case, forming the complex brings in the certain
structural rearrangements taking place both in the Carte-
sian and angular spaces. At the same time, the Cyc B
peptide experiences the more profound transformation of
its structure: so when we confront the V3 structures ma-
terialized in the overmolecular ensemble and in the un-
bound status, the values of cRMSD and aRMSD are
respectively 2.0 Å and 47 and, in the case of the Cyc B
peptide, the corresponding values rise to 4.0 Å and 57.
This observation falls into line with the supposition
above, whereby the Cyc B peptide, in spite of the rela-
tive conformational rigidity, may exhibit the higher
flexibility of the polypeptide chain on drastic medium
A. M. Andrianov et al. / HEALTH 2 (2010) 661-671
Copyright © 2010 SciRes. http://www.scirp.org/journal/HEALTH/
Figure 4. Overmolecular structure of the HIV-1 SA-V3 loop (balls) with the Cyc B peptide (tubes).
Table 3 . Geometric parameters of intermolecular H-bonds for the structural complex of the HIV-1 SA-V3 loop with the Cyc B
Distance (Å)
Distance (Å)
Arg-131 NH1 Asp-182 OD1 3.0 2.0
Arg-131 NH2 Asp-182 OD1 3.2 2.3
Arg-131 NH2 Asp-182 OD2 3.1 2.2
Gly-171 NH Asp112 OD1 2.9 1.9
Gln-181 NE2 Tyr-92 CO 2.8 1.8
Gln-181 NE2 Asp-112 OD1 2.8 1.8
Asp-251 NH Gly-282 CO 2.8 1.8
Lys-32 NZ Ile-301 CO 2.8 1.9
Thr-52 OG1 Arg-311 CO 2.7 1.7
Lys-72 NH Lys-101 CO 2.8 1.8
Lys-292 NZ Asp-291 CO 2.9 2.0
Footnote: Superscripts 1 and 2 denote the amino acids of V3 and the CycB peptide respectively.
In studies [30,31], we implemented the computer-aided
design of two molecules referred to as Cyc A and FKBP
peptides and, having analyzed their structural complexes
with the HIV-1 SA-V3 loop [32], disclosed that the Cyc
A peptide binds effectively to its immunogenic crown,
whereas the FKBP peptide prefers to interact with the N-
and C-terminal segments of the virus principal neutral-
izing determinant. The findings derived here bear wit-
ness that, unlike the molecules constructed previously
[30,31], the Cyc B peptide is able to mask the function-
Openly accessible at
A. M. Andrianov et al. / HEALTH 2 (2010) 661-671
Copyright © 2010 SciRes. Openly accessible at http://www.scirp.org/journal/HEALTH/
ally crucial amino acids both of the V3 central part and
of its stem stretches. Moreover, as compared to these
molecules, cooperation of the Cyc B peptide with V3
brings in the origin of more stable overmolecular struc-
ture: for instance, the value of the energy of intermo-
lecular interactions computed for the structural complex
of V3 with Cyc A peptide [31] totals -87 kcal/mol and, in
the case in question, it aggregates -350 kcal/mol (see
As shown in study [32], in spite of the hypervariabil-
ity of V3, its segments 3-7, 15-20, and 28-32 embracing
the highly conserved amino acids of gp120 give rise to
the closely related spatial backbone folds in different
virus isolates, and, therefore, they may be considered as
promising targets for anti-AIDS drug studies. Allowing
for these data in common with the evidence which bears
witness that the Cyc B peptide is capable of masking the
V3 functionally critical residues residing in its structur-
ally invariant segments, one may expect that synthetic
copy of this virtual molecule (or its structural analogs)
may display biological activity to various HIV-1 strains
exhibiting a broadly neutralizing effect. Beyond all
shadow of doubt, the peptide constructed here must ex-
perience the extensive experimental test to be considered
as the coming applicant for the role of “magic bullet”
displaying a wide-range blockade of the HIV-1 envelope
glycoprotein gp120.
In conclusion, the model of the structural complex of
Cyc B with V3 proposed above substantiates the litera-
ture data on a high affinity of immunophilins to V3 [13],
and the results derived from its analysis enable one to
make an optimistic prognosis of the prospects of using
their peptides as the starting chemicals for the design of
efficacious antiviral agents by protein engineering me-
This study was supported by grants from the Union State of Russia and
Belarus (scientific program SKIF-GRID; 4U-S/07-111) as well as
from the Belarusian Foundation for Fundamental Research (project
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