Accepted Manuscript

Assessing calix[n]arene as drug carriers for second generation

tyrosine kinase inhibitors by theoretical methods

Mohd Athar, Mohsin Y. Lone, Prakash C. Jha

PII: S0167-7322(17)33177-X
DOI: doi:10.1016/j.molliq.2017.09.113
Reference: MOLLIQ 7950
To appear in: Journal of Molecular Liquids
Received date: 16 July 2017
Revised date: 24 September 2017
Accepted date: 27 September 2017

Please cite this article as: Mohd Athar, Mohsin Y. Lone, Prakash C. Jha , Assessing
calix[n]arene as drug carriers for second generation tyrosine kinase inhibitors by
theoretical methods. The address for the corresponding author was captured as affiliation
for all authors. Please check if appropriate. Molliq(2017), doi:10.1016/
j.molliq.2017.09.113

This is a PDF file of an unedited manuscript that has been accepted for publication. As
a service to our customers we are providing this early version of the manuscript. The
manuscript will undergo copyediting, typesetting, and review of the resulting proof before
it is published in its final form. Please note that during the production process errors may
be discovered which could affect the content, and all legal disclaimers that apply to the
journal pertain.
 ACCEPTED MANUSCRIPT

Assessing calix[n]arene as Drug Carriers for Second Generation Tyrosine Kinase

Inhibitors by Theoretical Methods
Mohd. Athar1, Mohsin Y. Lone1& Prakash C. Jha*2

1
School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
2
Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar 382030, Gujarat, India

Mohd.Athar

PT
mathar@cug.ac.in
+917405498220

RI
MohsinYousuf Lone
mylonechem@cug.ac.in

SC
+919033526257

Prakash Chandra Jha

prakash.jha@cug.ac.in
NU
+918866823510

*Corresponding author:
MA

Dr. Prakash C. Jha,

Centre for Applied Chemistry,
Central University of Gujarat,
Gandhinagar-382030
D

Gujarat, INDIA
E

Email:prakash.jha@cug.ac.in
Telephone number: +91 8866823510
PT
CE
AC

1
 ACCEPTED MANUSCRIPT

Assessing calix[n]arene as Drug Carriers for Second Generation Tyrosine Kinase

Inhibitors by Theoretical Methods
Mohd. Athar1, Mohsin Y. Lone1& Prakash C. Jha*2
1
School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
2
Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
*Corresponding Author: E-mail: prakash.jha@cug.ac.in

Abstract

PT
With an endeavour to improve the bioavailability profile of Tyrosine kinase inhibitors (TKI’s) viz.
gefitinib, regorafenib and sunitinib, the drug carrier based on calix[n]arene macrocycles has been

RI
proposed. A total of 72 calix[n]arene-TKI’s complexes with the upper rim functionalized (SO3H, tert-
Butyl, iso-Propyl, COOH, C2H5OH, and C2H5NH2) calix[n]arene (n=4,5,6,8) were theoretically

SC
studied to form most probable inclusion complex. The subsequent intermolecular interactions were
explored by complementary-shape based method and Molecular Mechanics-Generalised Born
Molecular Volume (MM-GBMV) calculations. Based on the results, we articulate that the promising
NU
carrier for gefitinib (i-Pr/C2H5NH2-Calix[5]arene, t-Bu/i-Pr-Calix[6]arene and C2H5NH2/C2H5OH-
Calix[8]arene), sunitnib (SO3H/t-Bu/C2H5OH-Calix[8]arene, t-Bu-Calix[6]arene) and for
MA

regorafenib (C2H5OH-Calix[5]arene, t-Bu/i-Pr-Calix[6]arene and COOH-Calix[8]arene) have the

greater capability to act as drug carrier.
Keywords: Calixarene, inclusion complex, bioavailability, tyrosine kinases, interaction energy,
D

implicit solvation
E
PT

1. Introduction
Tyrosine Kinase Inhibitors (TKI’s) have proven to be effective for the treatment of lung
CE

cancer, chronic myeloid leukemia and gastrointestinal tumors[1, 2]. These inhibitors are
basically actuate by impeding phosphorylation and breaks the communication signals within
the cell to deregulate the cellular activity [3-5]. Therapeutic use of first generation TKI’s i.e.,
AC

Imatinib (GleevacTM) is continuously increasing which led to the development of drug

resistance. This adverse scenario prompted the investigators to think for other alternatives
that can provide improved ailment against the tyrosine kinases. In this course, Gefitinib,
sunitinib and regorafenib have tremendously attained much of the research focus (Figure 1).
This is due to their potentials for inhibiting tyrosine phosphorylation along with their ability
to bind against epidermal growth factor (EGF), Fibroblast growth factor (FGF) and Vascular
endothelial growth factor (VEGF) receptors. Besides, their preclinical testings have shown
encouraging results but their clinical aspects have still been underestimated. The possible

2
 ACCEPTED MANUSCRIPT

reason for this is their less bioavailability (~60%) and high protein binding capability (90-
95%); that makes them difficult to metabolize (Table 1). Moreover, improvement in the
specificity is also required so that administered drug can reach to the specified targeted
tissue[6, 7]. As a progressive step to improve the bioavailability profiling of the TKI’s, we
used in-silico approach (mentioned in Figure 1) to search for the suitable macrocycle based
drug carrier.

Maintaining the optimal drug-likeness and control release behavior is a crucial paradigm in

PT
vascular drug targeting [8]. Its importance can be analyzed by the numerous drug withdrawal
reports of FDA including gefitinib (a selective inhibitor of EGFR) in 2004 [9-11]. Moreover,

RI
the increasing resistance for TKI’s due to genetic mutations and ATP-bound cassette (namely

SC
ABCB1 and ABCG2) transporters has reported as major obstacles in TKI's drug discovery
[12-16]. As an immediate solution for bioavailability and drug solubilisation related issues,
there has been a growing interest for the development of drug carriers[17, 18]. As such, a
NU
drug carrier reduces the probability of sequestration and decreases the chances of resistance
development [19]. For designing such drug carrier ensembles (inclusion complex), we have
MA

selected calix[n]arene as hosts due to their inherent structural versatility. It has been reported
that calix[n]arene can provide higher retention rate to drug without hindering their diffusion
between cells[20].
D

Calix[n]arenes are a family of cyclooligomers of phenol-formaldehyde that exists as vase-like

E

structure and comprise a central annulus with an upper and a lower rim [21-26]. Notably, its
PT

central hydrophobic cavity can accommodate a variety of molecules, ions or metals via non-
bonded and bonding interactions [27]. Moreover, chemical stability, null toxicity, substitution
CE

ease, ability to change solubility [28-32], bioavailability and dissolution rate tempted us to
select calix[n]arene (n=4,5,6 and 8) as hosts in the present study. Recently, calix[n]arenes
AC

have been immensely studied for the inclusion complexation of warfarin [33],
niclosamide[34], furosemide [29], nifedipine[35], GTP[20] and testosterone [36]. The same
authors have claimed that suitability of all the drugs can be augmented and thereby the drugs
can easily attain better pharmacokinetics. Gelindo-Murillo et al. reported that cavity size of
calix[4,5,6,8]arene substantially affects the formation of inclusion complex with imatinib (a
potent TKI’s) [19] . It was also argued that upper rim sulphonic and ethoxy substituted
calix[n]arenes has the enhance tendency to form the inclusion complex with calix[5,6]arene.
Later on, the same investigators have extended their study to bosutinib and sorafenib drugs
[19, 37].

3
 ACCEPTED MANUSCRIPT

In this study, an attempt was made to explore the possibilities of inclusion complexes of
TKI’s within the diversified calix[n]arene framework to propose the appropriate drug carrier
(host) for TKI’s. For this appraisal, we have considered four types of hosts i.e., calix[n]arene
with n=4,5,6,8 that were ligated with six different electron-withdrawing and donating groups
(SO3H, tert-Butyl, iso-Propyl, COOH, C2H5OH, and C2H5NH2) at the upper rim. The
complexation ability was evaluated to anticipate that the suitable drug carrier can enrich the
activity of drug (bioaccumulation) and can meet the optimal bioavailability paradigms with

PT
minimal side effects.

RI
SC
NU
MA

Figure 1. Chemical Structures of Tyrosine kinase Inhibitors (TKIs)

E D
PT
CE
AC

Figure 2. Chemical structure and naming scheme for all hosts

2. Materials and Methods

4
 ACCEPTED MANUSCRIPT

The chemical structures of three TKI’s guest (sunitinib, gefitinib and regorafenib) (Table 1
and Table S1) and their protein binding information was collected from the Drugbank
(www.drugbank.ca) [38]. For calix[n]arene hosts, we tried to retrieve the crystal coordinates
from the earlier published reports i.e., t-butyl calix[4]arene (4b) [39], parent
calix[5]arene[40], t-butyl & iso-propyl calix[5]arene (2b, 2c) [41] and t-butyl calix[8]arene
(3b) [42] via Crystal Structure Database (CSD) [43]. But, out of 24 designed hosts (Table 2),
only four crystal structures were reported in the CSD. We, therefore, draw the derivative

PT
structures on the reported core moiety and subjected it for the geometry optimization at
Density Functional Theory (DFT) level of approximation using Gaussian 09 (Revision B.01)

RI
[44]. The B97D functional along with 6-31G(d) basis set was selected for the DFT
calculation. However, other hybrid functionals were tested but Grimme’s B97D provided the

SC
most reasonable convergence time with great accuracy [45]. Also, the cone conformer of the
calix[n]arenes was considered as starting structures for geometry optimizations [46, 47].
NU
The Blood Brain Barrier (BBB), Human Intestinal Absorption (HIA) and other ADME
descriptors of TKI’s were evaluated using the Discovery Studio Client v4.0 [48]. Aqueous
MA

solubility was computed using the model developed by Cheng et al. on 775 compounds [49].
HIA and BBB permeation was calculated by the model developed by Egan et al. [50, 51].
CYP2D6 enzyme inhibition and hepatotoxicity was calculated using the Susnow[52] and Xia
D

model [53]. Moreover, the plasma protein binding (PPB) was considered from Xia, Dixon
E

and Votano method [53-55].

PT

The searching for the most probable inclusion complex (of 1:1 stoichiometry) was made by
utilizing the patchdock, firedock and HexServer algorithms. At the PatchDock platform [56],
CE

TKI’s were considered as guest molecules and calix[n]arene as host (receptor). The platform
exploits the molecular shape complementarity docking fit transformations and predicts most
preferred complex structure. In particular, it considers the molecular Connolly dot surface as
AC

concave, convex or flat patches [57], and matches the constructed complementary patches to
produce the complex structure. Ranking of the poses were carried out in terms of geometric
fit, approximate interface area size, atomic contact energy and desolvation patches [58].
Thereafter, the non-redundant docking solutions were delineated from redundant solutions
via root mean square deviation (RMSD) based clustering. Further, all the docking solutions
were subjected for refinement and rescoring by firedock[59] that re-refine the complex
structure by incorporating the minor flexibility. Moreover, the structures of the inclusion
complexes were also generated by Hex software v6.3 that employs Fourier transform (FFT)

5
 ACCEPTED MANUSCRIPT

and rotational correlations [60] to refine the feasible docking mode [61, 62]. The full list of
parameters is given in Table S2. Thereafter, the docked poses were clustered into different
groups and the inclusion complexes with lowest energy conformations were selected and
analyzed. For visualization purposes, the Discovery Studio Client v4.0[48] program was
utilized.
Considering the role of solvation on the structure, energetics, and dynamics of the inclusion
complex, we used the implicit solvation method in order to include the polar and non-polar

PT
effects caused by solvent (water)[63]. Compared to explicit solvation, implicit solvation
method uses less volume (85%) with affordable computational cost[64, 65] The free host,

RI
guest and constructed inclusion complexes were all subjected for energy minimization in an
implicit solvent (water) using CHARMM22 force field[66] with a constant dielectric

SC
constant treatment of 1 [67-69]. It is worth to mention that CHARMM22 geared suitable
results with conformational interconversions of calix[4]arene and reproduced the self
NU
inclusion of O-alkyl-calix[6]arene[70, 71]. The solvation approach uses conventional
Molecular Mechanics (MM) method to compute various energy terms (total potential, van
MA

der Waal, electrostatic energy) and particularly the effective born radii; as calculated by
numerical integration of molecular volume (MM-GBMV). GBMV approach includes the
higher order correction term to the coulomb field approximation in order to improve the
D

radii description of Poisson-Boltzmann [72, 73]. Smart minimizer (combination of steepest

E

descent and conjugate gradient) algorithm with RMS gradient and minimizing steps of 0.001
PT

and 5000 respectively were used. Moreover, non-polar surface constant, non-polar surface
coefficient, non-bond radius cut-off distance of 0.92, 0.00542 and 10Å respectively with
CE

SHAKE constraint were considered for the simulation.

Based on MM-GBMV calculations, we calculate the complexation energies (interaction
energies, Eint), as the energy difference between the resulting complex with the energy sum of
AC

the isolated host and guest) were computed according to the Eq. 1.
𝐸𝑖𝑛𝑡 = 𝐸𝑐𝑜𝑚𝑝𝑙𝑒𝑥 − (𝐸ℎ𝑜𝑠𝑡 + 𝐸𝑇𝐾𝐼 ) Eq. 1
where 𝐸𝑖𝑛𝑡 , 𝐸ℎ𝑜𝑠𝑡 and 𝐸𝑇𝐾𝐼 represent the total energy of the complex, the free optimized host
and the free optimized TKI’s energy respectively.

3. Results and Discussions

3.1 Bioavailability profiling

6
 ACCEPTED MANUSCRIPT

Early preclinical studies of sunitinib, gefitinib and regorafenib have reflected their marked
ability to inhibit tyrosine kinases receptor. Also, in order to be an effective drug, the drug
should have ideal ADME and bioavailability profiling [8, 74] to avoid later stage attritions
[75]. Therefore, the related parameters i.e., aqueous solubility, HIA, BBB permeation etc.
were appraised (Table 1) [50]. The aqueous solubility of regorafenib was observed to be
appropriate (level 1) but sunitinib and gefitinib lack the aqueous solubility (level 2) [49].
However, BBB penetration of regorafenib was under-define (level 4) followed by moderate

PT
for sunitnib (level 2) and good for gefitinib (level 1). The quantitative estimate of drug-
likeness (QED)[76] which is an overall ensemble of ADMET was reported to be 0.555, 0.454

RI
and 0.627 for gefitinib, regorafenib and sunitinib respectively on the maximum scale of 1.
Overall, drug-likeness of TKI’s clearly indicates that there is need to augment the molecular

SC
properties by employing the possible ways [77, 78]. Furthermore, the AlogP value of
regorafenib and gefitinib was observed to be >4.2 that clearly suggests the predominance of
NU
hydrophobic nature. Sunitinib reports the AlogP value of 2.99 that certainly articulate its
equal tendency to be partitioned in the hydrophobic and hydrophilic environment.
MA

Table 1. Bioavailability and drug-likeness parameters of the gefitinib, regorafenib and

sunitinib
Name Gefitib Regorafenib Sunitinib
Solubility_Level 2 1 2
D

BBB_Level 1 4 2
CYP2D6 2.41414 -4.62438 -1.16486
E

Hepatotoxic -3.99306 0.144049 -3.25333

PPB 2.80835 7.1701 -6.78108
PT

ADMET_PSA_2D 65.474 93.223 78.629

QED 0.55565 0.45461 0.62774
ALogP 4.203 4.381 2.997
CE

Molecular_PolarSurfaceArea 68.74 92.35 77.23

ADMET_BBB 0.109 - -0.472
Absorption_Level 0 0 0
Bioavailability (%) 59% 69-83 -
AC

Protein Bound 90% 99.5% 90-95

ADMET Aqueous Solubility: Predicts the solubility of each compound in water at 25°C and reports the predicted solubility
and a ranking relative to the solubilities of a set of drug molecules; Blood Brain Barrier: Predicts the blood-brain barrier
penetration of a molecule, defined as the ratio of the concentrations of solute (compound) on the both sides of the membrane
after oral administration, and reports the predicted penetration as well as a classification of penetration level; ADMET
CYP2D6 Binding: Predicts cytochrome P450 2D6 enzyme inhibition and reports whether or not a compound is likely to be
an inhibitor, as well as a probability estimate for the prediction (cut-off Bayesian score of 0.161); ADMET Hepatotoxicity:
Predicts the occurrence of dose-dependent human hepatoxicity (cut-off Bayesian score of -0.4095), PPB is the plasma
protein binding (cut-off Bayesian score of -2.209); QED is quantitative estimate of drug-likeness (Bickerton, G. Richard, et
al. "Quantifying the chemical beauty of drugs."Nature chemistry 4.2 (2012): 90-98); and PSA is the polar surface area (Å2).
ADMET Absorption: Predicts Human Intestinal Absorption (HIA) after oral administration and reports a classification of
absorption level

On the other hand, CYP2D6 enzyme inhibitor score was found to be higher for gefitinib
(2.414) than sunitinib (-1.16) and regorafenib (-4.624). Considering the cut-off bayesian

7
 ACCEPTED MANUSCRIPT

score (Table 1), it can be suggested that gefitinib can act as a CYP2D6 inhibitor. Moreover,
calculated 2D-PSA for regorafenib (93.22) was higher than gefitinib (65.47) and sunitinib
(78.62). Importantly, all the three TKI's were found to be greatly protein bound (90-95%) and
their overall bioavailability were close to 60% that can be attributed to the large magnitude
of plasma protein binding (PPB) (Table 1). This limited bioavailability profiling of the three
TKI’s led us to contemplate for the strategies that can enhance the bioavailability paradigms
and help in achieving better therapeutics with TKI’s.

PT
3.2 Shape-based fitting
The geometries of the hosts (upper rim functionalized calix[4,5,6,8]arenes) and the TKI’s

RI
(sunitinib, gefitinib and regorafenib) were optimized for their structural orientation in the gas

SC
phase at the B97D/6-31G(d) level. The selection of the level of theory for the calculation was
chosen from the earlier assessments and the adequacy of the B97D functional to handle
NU
dispersion interactions of π electron clouds [20, 79]. The optimized structures of the free
hosts and guests were given as input for generating the probable structures of inclusion
complexes using shape-based complementary fitting approach (rigid body docking)[80].
MA

Table 2. Energies of complexation for shape and electrostatic fit of the inclusion complexes
of calix[n]arenes and TKI’s computed using two different algorithms
D

Calix[4]arenes Calix[5]arene Calix[6]arene Calix[8]arene

E

Efd Hhs Efd Hhs Efd Hhs Efd Hhs

Regorafenib
PT

SO3H -280.16 -199.53 -33.48 -230.78 -36.35 -257.17 -42.26 -298.34

tBu -263.05 -200.46 -33.21 -222.46 -34.81 -270.27 -48.36 -306.81
iPr -281.8 -186.87 -37.01 -225.11 -38.48 -276.36 -43.64 -262.67
CE

COOH -241 -206.04 -32.97 -225.58 -32.53 -254.62 -42.41 -279.63

CH2CH2OH -158.39 -179.1 -36.19 -237.07 -27.15 -229.46 -40.08 -279.33
CH2CH2NH2 -177.76 -187.72 -43.04 -238.03 -35.15 -236.77 -32.38 -285.62
Sunitinib
AC

SO3H -43.76 -198.1 -47.25 -217.34 -34.78 -238.9 -39.5 -269.95

tBu -35.89 -186.62 -41.83 -209.99 -44.26 -266.19 -39.61 -286.63
iPr -24.92 -172.77 -34.3 -210.92 -36.08 -243.38 -42.18 -275.1
COOH -36.62 -196.45 -38.04 -222.09 32.33 -250.68 -34.17 -278.58
CH2CH2OH -16.45 -173.42 -.45.05 -234.17 -31.31 -223.02 -36.92 -257.15
CH2CH2NH2 -29.31 -188.61 -40.38 -243.81 -39.03 -256.02 -46.07 -269.49
Gefitinib
SO3H -27.66 -221.13 -42.84 -252.42 -35.77 -242.26 -37.66 -274.63
tBu -27.6 -206.81 -33.96 -253.96 -35.29 245.8 -43.62 -274.25
iPr -26.85 -190.58 -38.31 -242.26 -35.67 -242.26 -40.88 -273.56
COOH -34.67 -236.93 -40.22 -269.06 -36.38 -235.2 -39.47 -273.41
CH2CH2OH -1.18 -191.91 -33.55 252.02 -34.81 -226.58 -35.25 -270.79
CH2CH2NH2 -29.79 -201.33 -45.92 258.29 -35.83 -229.42 -35.46 -269.76
*Efd indicates Firedock global energy (kJ/mol) and Hhs indicates HexServer Scores (kJ/mol)

8
 ACCEPTED MANUSCRIPT

It was assumed that inclusion complex formation does not affect the structure of either
molecule [81], we, therefore, kept the internal coordinates of both hosts and guests as fixed
during the docking. Moreover, the shape based complementary fit calculations were carried
out in gas phase due to the fact that the complexation interactions in the solution are mainly
governed by the gaseous phase components [82, 83]. Besides, all host and guest chemical
space and mode of interactions were taken into account during docking experiments. For this
reason, we used three methods for docking; first and second were patchdock and firedock that

PT
uses robust, global and soft rigid body docking via surface patch matching algorithm [84].
However, HexServer docking platform was also used that uses the spherical polar 5D-FFT

RI
translation-correlations. It is interesting to note that the similar methodology was applied on
recently published chlorhexidine-calix[4]arene inclusion complex and have reported comparable

SC
results [85].

The docking results of calix[n]arene-TKI’s inclusion complexes mentioned in Table 2

NU
indicate preference of the host for the TKI’s greatly varies with the calix rings size and the
appended substituents. As per the patchdock/firedock shape complimentary fitting algorithm,
MA

we observed that sunitinib has greater ability to form an inclusion complex with 1a (-47.25
kJ/mol), 3f (-46.07 kJ/mol), 1e (-45.05 kJ/mol) and 2b (-44.26 kJ/mol) as illustrated in Table
2 and Table S3. The 5-fluoro-2-oxo indole group of sunitnib form an ideal complex with the
D

preformed cavity of 1a. A similar interaction with the bent shaped calix was also observed for
E

the 1e host. Moreover, t-Bu substituted calix[6]arene form extended bimodal type structure
PT

that positions the sunitinib at its extended upper arm. Further, the flattening of the host in
calix[8]arene was reported calix[8]arenes hosts i.e., 3f that resultantly forms the inclusion
CE

complex in planar/sandwiched orientation. The third docking platform, i.e. HexServer, also
complements the above findings. The obtained scores suggests that the shape fitting of
AC

sunitinib with calix[n]arenes host increases with ring size (n=4, 5, 6, 8) in general. However,
for particular ring size, it prioritizes SO3H for calix[4]arene, C2H5OH/NH2 for calix[5]arene
and t-Bu for calix[6,8]arene. The detailed scores and contribution of different energy terms
towards overall binding potentials are depicted in Table S3.

Regorafenib inclusion complexation with patchdock/firedock and HexServer FFT algorithms

also provides significantly correlated results. The hosts 3b (-48.36 kJ/mol), 3c (-43.64
kJ/mol), 1f (-43.04 kJ/mol), 4a (-38.37 kJ/mol) and 1e (36.69 kJ/mol) were the most
energetically (higher global energies) bound calix[n]arene carriers for the regorafenib (Table

9
 ACCEPTED MANUSCRIPT

2, S4). Even though the bulkier groups (t-Bu and i-Pr) appended hosts contributes to the
repulsive term, their attraction term overweight the effect and exhibit stable complexes
(Table S4). Further, from the HexServer results (Table 2), it can be argued that SO3H and
COOH substituted hosts for calix[4]arene, C2H5OH/NH2 for calix[5]arene, t-Bu/i-Pr for
calix[6]arene and SO3H/t-Bu for the calix[8]arene are much more suitable for regorafenib
complexation.

Binding energies for the best docked solutions for gefitinib were ranked as 1f (-45.92

PT
kJ/mol), 1a (-42.84 kJ/mol), 3c (-40.88 kJ/mol) and 3d (-39.47 kJ/mol) and 2d (-36.38
kJ/mol) hosts (Table 2, S5). In 1f-gefitinib complex, inclusion occurs through 3-chloro-4-

RI
fluorophenyl and quinazolinamide; however, it is supported by the morpholine ring in 1a.

SC
Further, in calix[8]arene hosts (3c and 3d), flat and planar orientation was observed. FFT
translation-correlation (HexServer) also prioritize the same order i.e., for calix[4]arene (4a,
4c), calix[5]arene (1d, 1f) and for calix[8]arene (2a, 2b).
NU
MA
E D

Figure 3. Possible insertion modes observed in calix[4,5,6,8] arenes-TKI’s inclusion

PT

complexes
CE

3.3 Binding Mode Characterization

The binding modes were characterized based on interaction component and chemical space
AC

occupied by the hosts and guest (Figure 3). We therefore, categorised the complexes as type
A in which drug (TKI’s) positions at the lower rim (i.e. OH groups), type B for upper rim,
type C for inside the ring, type D for sideways or peripheral and type P for the parallel or
sandwiched orientation to the calix[n]arenes (Figure 3). The details of all the insertion modes
are tabulated in Table 3.

It has been shown that lower rim calix[4,5]arenes were predominantly exhibited type B, type
C and type D interaction type with TKI’s. On the contrary, type P and type D of insertion
mode were majorly reported in higher calix[8]arenes. Nevertheless, we perceived the mixed
type of orientation and interaction in calix[6]arenes. It is also needed to emphasize that no

10
 ACCEPTED MANUSCRIPT

apparent selectivity in the orientation was analyzed with the particular calix[n]arene and
TKI’s. Even though, type B interaction for sunitinib and type B/C interaction for gefitinib
were specifically dominant in calix[4,5,6]arenes.

Table 3. Insertion modes of the representative structure from the most populated cluster for
each of the complexes
Calix[4]arenes Calix[5]arene Calix[6]arene Calix[8]arene
Regorafenib

PT
SO3H B+P A+P P P+D
tBu D B+C B+C P
iPr A C P P+D

RI
COOH B B P D
CH2CH2OH A B+C A+D D

SC
CH2CH2NH2 D B+C P P+D
Sunitinib
SO3H B+C B+C B+C P+D
tBu C P+B P+B P+D
NU
iPr C B B P
COOH B B B P
CH2CH2OH B+D A A P
CH2CH2NH2 B+C P P P
MA

Gefitinib
SO3H B+C C B B+C
tBu C C C D
iPr C C B+P P+D
D

COOH B B+C B+D P+D

CH2CH2OH C C D P+D
E

CH2CH2NH2 B+D B+D B+C P+D

PT

3.4 Molecular Mechanics-Generalized Born Molecular Volume (MM-GBMV)

Solvation
CE

3.4.1 Gefitinib
The MM-GBMV calculations were performed along with implicit solvation to estimate the
AC

interaction energies of calix[n]arene-TKI’s complexes. Calix[4]arene shows greater

complexation ability with gefitinib particularly via t-Bu and C2H5NH2 substitutions i.e., -
43.33 and -48.56 kcal/mol respectively (Table S6, Figure 4). The 3-Chloro-4-fluorophenyl
fragment was inserted into the cavity to form favourable π interactions i.e., T-shaped π-π and
π-sigma contacts (Figure S1). The interaction was also actuated by fluorine that additionally
forms π-lone pair contact with the calix[4]arene.
In the case of 4f, gefitinib pierced/inserted into the cavity of calixarene to a greater extent and
therefore, additionally generates the π interactions with the ring (quinazolin-4-ylamine).
Complementary to this, the SO3H-calix[4]arene (4a) develop less stable complex structure (-

11
 ACCEPTED MANUSCRIPT

17.34 kcal/mol) as the favourable inclusion complex was generated with the morpholine ring
by utilizing weak π-sulphur contact with the gefitinib (Figure S1). Likewise, 4e and 4c also
engender the complex with moderate energies (-39 to -34 kcal/mol) that suggests its
favourability for the optimal drug release (Figure 4, Table S6).
Compared to other calix[n]arenes, calix[5]arenes exhibit significant binding energies with
gefitinib. We believe that increase in binding energies of calix[5]arene is due to its open vase
and a larger cavity that allows the drug to interact via non-bonded interaction. In particular,

PT
1b, 1c and 1d have the larger interaction energies i.e., -60.04, 59.43 and -61.35 kcal/mol
respectively. It was also observed that 1b and 1d host form the complex via the two main

RI
counterparts viz. morpholine and 3-chloro-4-fluorophenyl ring. Subsequently, the larger part
of the drug renders inside calix cavity, as a result, their complexation energies emerges out to

SC
be higher (Figure 4(a), Figure S1).
Exceptionally, low interaction energy of 1a-gefitinib complex (-19.43kcal/mol) was due to
NU
the larger weight of the potential energy (-317.66 kcal/mol) and electrostatic energy (-256.92
kcal/mol) of free 1a host that cancels out the energy terms of the complex (E.q. 1) (Table S6).
MA

For the complexation, this large barrier is difficult to disrupt and as a result, it presents only
weak non-classical hydrogen bonding via SO3H donors. Similar to calix[4,5]arene, t-Bu and
i-Pr analog of calix[6]arene (2b and 2c) were also succeeded to own relatively larger
D

capability to bind with the gefitinib i.e., -52.70 and -55.45 kcal/mol. The 2b prominently
E

interacts through π-π stacking and T-shaped π-π interactions with calixarene along with
PT

intramolecular hydrogen bonds (Table S1, Table S9). However, in 2c, the quinazoliniamine
ring orients outwards to the cavity and thereby forms π-π stacking interactions via two rings
CE

of 2e. Complementary to this, the most interesting trend was observed with 2f that has
remarkably larger Eint of -121.29 kcal/mol (Table S9). Specifically, the host 2f form two
strong hydrogen bonds with NH donor and OH acceptors along with π type interactions
AC

(Figure S1).
3.4.2 Regorafenib
The regorafenib displays unpromising interaction energy with SO3H analog of the
calix[4]arene, 4a as depicted from Figure 4 and Table S7. However, as the calix rings
increases to calix[5]arene particularly in SO3H-calix i.e., 1a, it marks substantial
complexation ability with the drug (-55.83 kcal/mol). This is due to the appropriateness in the
shape and size of the host (calix[4]arene) and guest (regorafenib). For this reason, it was
apparent to observe that calix[8]arene (3a) exhibits greater stabilizing interactions. Besides,

12
 ACCEPTED MANUSCRIPT

the essentially involved type P orientation was majorly governed by π-π contacts, hydrogen
bonding and π-hydrophobic interaction in 3a (-63.97). Thus, it can be further argued that
extended and bent hosts are more favoured for regorafenib (Figure S2).

PT
RI
SC
NU
MA
D

Figure 4: Energies of Calix[4,5,6,8]arenes-TKI’s inclusion complexes (in Kcal/mol)

E

obtained from the Molecular Mechanics-Generalized Born Molecular Volume (MM-GBMV)

PT

Solvation

It can also be demonstrated from Table 4(b) that calix[8]arene in general shows the greater
CE

affinity for regorafenib. Likewise, the similar binding capability was also observed for i-Pr
and t-Bu analog of calix[4,5,6,8]arene. However, 1a comprises high interaction energy (-
55.83kcal/mol) and interact via type A through the lower rim. As illustrated from Figure S2,
AC

it utilizes the carbonyl oxygen to form strong H-bonds with lower rim OH of calix 1a.
Moreover, comparable binding potentials were also observed for 1d (-47.75kcal/mol). It was
further observed that among calix[6]arene analog only 2b and 2a were able to generate
complexes with significantly larger energies i.e., -52.85 and -46.53 kcal/mol respectively
(Table S9). The rod-shaped regorafenib occupy the extended cavity of 2b and stabilizes
through π- π stacking and π-hydrophobic interactions (FigureS2). The SO3H substituted
calix[8]arene has the highest Eint i.e., -63.97 kcal/mol and efficiently forms five strong
hydrogen bonds (Table4 ) with SO3H and lower rim oxygens. Similarly, 3c also form three

13
 ACCEPTED MANUSCRIPT

strong hydrogen bonds utilizing fluorine donor and NH acceptor. With this observation, it can
be claimed that planar configuration of larger rims are much more suited for inclusion
complexation of regorafenib. Summing up the results, we reported that 1a, 2b, 2c and 3d are
the most promising hosts for regorafenib that needs to be tested for their release into the
mainstream.

3.4.3 Sunitinib
Sunitinib was observed to exhibit moderate binding potentials compared to gefitinib and

PT
regorafenib in general. Subsequently, their energies with 4c, 4d and 4e were -32.96, -31.79
and -34.61 kcal/mol respectively (Figure 4, Table S8). Further, their respective energy

RI
contribution from the various energy terms i.e., potential energy, van der Waals energy and

SC
electrostatic energy has been given in Table S8. In the modeled complexes, 4c exhibit T-
shaped π-π interaction with a fluoro-phenyl fragment of sunitinib along with intramolecular
hydrogen bonding signatures (Figure S3). Similarly, 4e occupies the same chemical space
NU
and hence display the similar interaction profile. Moreover, 4d positioned at the lower rim
and located at the whole cavity length of calix[4]arene. The host developed H-bonding with
MA

COOH acceptor and π as well as sigma-π/π-π stacking interactions with sunitinib. On the
other hand, 4f was unable to occupy the favourable binding space and therefore has the less
energies (-22.71 kcal/mol).
D

Among calix[5]arene, 1b, 1d and 1e succeeded to form optimal inclusion complex with
E

sunitinib i.e., -41.47, -37.53 and -41.73 kcal/mol respectively. Both hosts (1b and 1e)
PT

subjugated the similar chemical space and form inclusion complex via a 5-fluoro-2-oxoindole
fragment of sunitinib (Figure S3). Notably, the drug orients parallel to the cavity in 1b while
CE

it situates perpendicular to the cavity in 1e and 1d. The major interactions in 1d can be
simplified as π-π contacts via pyrrole ring of sunitinib. It has been found that 2c was unable
AC

to orient properly within the cavity of host and therefore only displayed weak interaction
energies (-16.66 kcal/mol) (Figure S3).
Calix[8]arene manifested prominent binding ability with enhanced interaction energies for
3a, 3b and 3e hosts in particular, i.e., -59.58, -56.37 and -47.10 kcal/mol respectively (Table
S9). Because of the presence of eight rings, the shape of calix[8]arene is largely planar and
cavity size decreases (Figure S4). For this reason, it provides less steric protection for the
hydrophobic drug but also at the same time offers larger surface area for the interaction.
Owing to it, we have obtained larger interaction energies for the calix[8]arene system for all
the TKI’s. For the present case, 3a form the sandwiched structure through the two rings of

14
 ACCEPTED MANUSCRIPT

fluoro-phenyl and indole ring of sunitinib and develop a common pattern of π-interactions
with 3a, 3b and 3c.
As per one of the reviewer suggestion, we have examined the effects on the polarities (dipole
moment) in solvation and aquous phases. For that, energy calculations were performed on the
representative calix[5]arene-TKI’s complexes at the B97D/3-21G(d) level (Table S10 ). It
has been suggested by Ordaz et al. [86] that increase in complex polarity offers the condition
of improved solubility and dispersion. In analogous to it, TKI’s complexes with 1b, 1d and

PT
1e calixarenes displayed increase in the polarities on solvation. Further, we anticipate that
polarity change of ~2 D will led to the dissolution of the complexes in the buffering

RI
environment of the biological system.

SC
3.5 Promising candidates for the Drug carrier for TKI’s
Owing to the fact, that a drug carrier should form a stable and labile complex intended for the
NU
proper release[37], we selected and identified the complexes based on interaction energy
(Eint) values. The complexes with >-45 to <-60 kcal/mol for regorafenib and sunitinb, and >-
MA

50 to <-60 kcal/mol for gefitinib were considered as suitable drug carrier complexes (Figure
4). We assume that little control over the insertion is achievable under such conditions
experimentally. Following such assumption, we articulated that the proposed host for
D

gefitinib (i-Pr/C2H5NH2-calix[5]arene, t-Bu/i-Pr-calix[6]arene and C2H5NH2/C2H5OH-

E

calix[8]arene), sunitnib (SO3H/t-Bu/C2H5OH-calix[8]arene, t-Bu-calix[6]arene) and

PT

regorafenib (C2H5OH-calix[5]arene, t-Bu/i-Pr-calix[6]arene and COOH-calix[8]arene) have

the greater capability to act as drug carrier.
CE

Conclusion
AC

The paper presents a novel way of analysing the possibilities of the complexation potential of
TKI’s by the macrocycle carrier. From the outcome of our investigation it can be concluded
that there is no apparent selectivity in the orientation and insertion mode for a calix[n]arene
(n=4, 5, 6, 8) with TKI’s (gefitinib, sunitinib and regorafenib). Even though, for the majority
of the cases, we were able to observe that sunitinib form the complexes via upper rim (type
B) whereas, gefitinib utilizes combined mode i.e., upper rim and inside the ring (type B/C);
that remain specifically dominant in calix[4,5,6]arenes. An important implication of these
findings is that the dominance of an interaction type is related to the structural orientation of

15
 ACCEPTED MANUSCRIPT

guest and host molecules forming the inclusion complex. Essentially, not only the
substituents (SO3H, t-Bu, i-Pr, COOH, C2H5OH, and C2H5NH2) that decides the dominance
of the interation types; rather it is the associative nature of corresponding calixarene and drug
configurations [87]. For this reason, we have not reported specific trend in the substituted
calix[n]arene for a particular TKI’s.
Moreover, due to the flattening of the calix[8]arene host, it forms the planar/sandwiched
orientation in majority of the cases. Interaction energies, as calculated using the MM-GBMV

PT
method, roughly increase with increasing n in the calix[n]arene, and usually exhibit larger
values for R = SO3H and C2H5NH2. We believe that higher coordinating nature of the

RI
substituent at the upper rim yield the most stable complexes over the less coordinating
substituents. Within our studied chemical space, calix[n]arenes with n = 6 and 8 are the most

SC
promising drug carriers owing to their ability to wrap around the TKI’s and thereby maximize
non-bonded interactions. Overall, we concluded that the promising hosts for gefitinib (i-
NU
Pr/C2H5NH2-calix[5]arene, t-Bu/i-Pr-calix[6]arene and C2H5NH2/C2H5OH-calix[8]arene),
sunitnib (SO3H/t-Bu/C2H5OH-calix[8]arene, t-Bu-calix[6]arene) and for regorafenib
MA

(C2H5OH-Calix[5]arene, t-Bu/i-Pr-calix[6]arene and COOH-calix[8]arene) has greater

ability to act as drug carrier for the respective TKI’s. The findings suggest that this approach
could be useful for designing the inclusion complexes for the respective hosts. Further
D

research is desirable to validate the predictions at higher level of theory or by experimental/

E

clinical means to acclaim the potentials.

PT

Acknowledgement
CE

The authors gratefully acknowledge the generous financial support by Department of Science
& Technology (DST), New Delhi under INSPIRE-JRF grant (Reg. No. IF150167) awarded to
AC

Mohd Athar. Prakash C. Jha would also like to thank SERB, DST for the project grant
(EMR/2016/003025). The authors would also like to thank their colleagues Prabodh Ranjan,
Anu Manhas for their valuable insights and recommendations. Moreover, Central University
of Gujarat-Gandhinagar (CUG) is also greatly acknowledged for providing basic
infrastructure and computational facilities.

Declaration of interest statement

The authors declare no conflict of interests regarding the publication of this paper.

16
 ACCEPTED MANUSCRIPT

References

1. Arora, A. and E.M. Scholar, Role of tyrosine kinase inhibitors in cancer therapy. J Pharmacol
Exp Ther, 2005. 315(3): p. 971-9.
2. Pawson, T., Regulation and targets of receptor tyrosine kinases. Eur J Cancer, 2002. 38
Suppl 5: p. S3-10.
3. Posner, I., et al., Kinetics of inhibition by tyrphostins of the tyrosine kinase activity of the
epidermal growth factor receptor and analysis by a new computer program. Molecular
pharmacology, 1994. 45(4): p. 673-683.
4. Polier, S., et al., ATP-competitive inhibitors block protein kinase recruitment to the Hsp90-
Cdc37 system. Nature chemical biology, 2013. 9(5): p. 307-312.

PT
5. Levitzki, A. and E. Mishani, Tyrphostins and other tyrosine kinase inhibitors. Annu. Rev.
Biochem., 2006. 75: p. 93-109.
6. Torchilin, V.P., Drug targeting. European Journal of Pharmaceutical Sciences, 2000. 11: p.
S81-S91.

RI
7. Bae, Y.H. and K. Park, Targeted drug delivery to tumors: myths, reality and possibility.
Journal of Controlled Release, 2011. 153(3): p. 198.

SC
8. Athar, M., M.Y. Lone, and P.C. Jha, First protein drug target’s appraisal of lead-likeness
descriptors to unfold the intervening chemical space. Journal of Molecular Graphics and
Modelling, 2017.
9. Cohen, M.H., et al., FDA drug approval summary: gefitinib (ZD1839)(Iressa®) tablets. The
NU
oncologist, 2003. 8(4): p. 303-306.
10. FDA, U. Gefitinib (marketed as Iressa) Information. Available from:
https://www.fda.gov/Drugs/DrugSafety/PostmarketDrugSafetyInformationforPatientsandProv
iders/ucm110473.htm.
MA

11. Onakpoya, I.J., C.J. Heneghan, and J.K. Aronson, Post-marketing withdrawal of 462
medicinal products because of adverse drug reactions: a systematic review of the world
literature. BMC medicine, 2016. 14(1): p. 10.
12. Chapuy, B., et al., ABC transporter A3 facilitates lysosomal sequestration of imatinib and
D

modulates susceptibility of chronic myeloid leukemia cell lines to this drug. haematologica,
2009. 94(11): p. 1528-1536.
E

13. Druker, B.J., Translation of the Philadelphia chromosome into therapy for CML. Blood,
2008. 112(13): p. 4808-4817.
PT

14. Eechoute, K., et al., Drug transporters and imatinib treatment: implications for clinical
practice. Clinical Cancer Research, 2011. 17(3): p. 406-415.
15. Takahashi, N., et al., Influence of CYP3A5 and drug transporter polymorphisms on imatinib
CE

trough concentration and clinical response among patients with chronic phase chronic
myeloid leukemia. Journal of human genetics, 2010. 55(11): p. 731-737.
16. van Erp, N.P., H. Gelderblom, and H.-J. Guchelaar, Clinical pharmacokinetics of tyrosine
kinase inhibitors. Cancer treatment reviews, 2009. 35(8): p. 692-706.
AC

17. Campone, M., et al., Phase I and pharmacokinetic trial of AP5346, a DACH–platinum–
polymer conjugate, administered weekly for three out of every 4 weeks to advanced solid
tumor patients. Cancer chemotherapy and pharmacology, 2007. 60(4): p. 523-533.
18. Jun, Y.J., et al., Selective tumor targeting by enhanced permeability and retention effect.
Synthesis and antitumor activity of polyphosphazene–platinum (II) conjugates. Journal of
inorganic biochemistry, 2005. 99(8): p. 1593-1601.
19. Galindo-Murillo, R., M.E. Sandoval-Salinas, and J. Barroso-Flores, In silico design of
monomolecular drug carriers for the tyrosine kinase inhibitor drug imatinib based on calix-
and thiacalix [n] arene host molecules: a DFT and molecular dynamics study. Journal of
Chemical Theory and Computation, 2014. 10(2): p. 825-834.
20. Galindo-Murillo, R., et al., Calix [n] arene-based drug carriers: a DFT study of their
electronic interactions with a chemotherapeutic agent used against leukemia. Computational
and Theoretical Chemistry, 2014. 1035: p. 84-91.

17
 ACCEPTED MANUSCRIPT

21. Mutihac, L., et al., Complexation and separation of amines, amino acids, and peptides by
functionalized calix [n] arenes. Journal of inclusion phenomena and macrocyclic chemistry,
2005. 51(1-2): p. 1-10.
22. Mohammed-Ziegler, I. and A. Grün, Complex formation between aliphatic amines and
chromogenic calix [4] arene derivatives studied by FT–IR spectroscopy. Spectrochimica Acta
Part A: Molecular and Biomolecular Spectroscopy, 2005. 62(1): p. 506-517.
23. Memon, S., et al., Polymer supported calix [4] arene derivatives for the extraction of metals
and dichromate anions. Journal of Polymers and the Environment, 2003. 11(2): p. 67-74.
24. Fehlinger, M. and W. Abraham, Calix [4] arenes bearing a tropylium substituent as hosts for
organic cations. Journal of Inclusion Phenomena and Macrocyclic Chemistry, 2007. 58(3-4):
p. 263-274.
25. de Namor, A.F.D., et al., The various factors involved in the extraction of alkali metal

PT
picrates by calixarene ester derivatives in the mutually saturated water–dichloromethane
solvent system. Physical Chemistry Chemical Physics, 2000. 2(19): p. 4355-4360.
26. Budka, J., et al., Urea derivatives of calix [4] arene 1, 3-alternate: an anion receptor with

RI
profound negative allosteric effect. Tetrahedron Letters, 2001. 42(8): p. 1583-1586.
27. de Fátima, Â., S.A. Fernandes, and A.A. Sabino, Calixarenes as new platforms for drug
design. Current drug discovery technologies, 2009. 6(2): p. 151-170.

SC
28. Patel, M.B., et al., Effect of p-sulfonatocalix [4] resorcinarene (PSC [4] R) on the solubility
and bioavailability of a poorly water soluble drug lamotrigine (LMN) and computational
investigation. RSC Advances, 2013. 3(36): p. 15971-15981.
NU
29. Yang, W. and M.M. Villiers, Aqueous solubilization of furosemide by supramolecular
complexation with 4‐sulphonic calix [n] arenes. Journal of pharmacy and pharmacology,
2004. 56(6): p. 703-708.
30. Panchal, J.G., R.V. Patel, and S.K. Menon, Preparation and physicochemical
MA

characterization of carbamazepine (CBMZ): para-sulfonated calix [n] arene inclusion

complexes. Journal of Inclusion Phenomena and Macrocyclic Chemistry, 2010. 67(1-2): p.
201-208.
31. Yang, W., et al., Effect of para-sulfonato-calix [n] arenes on the solubility, chemical stability,
D

and bioavailability of a water insoluble drug nifedipine. Current drug discovery technologies,
2008. 5(2): p. 129-139.
E

32. Shinkai, S., Calixarenes as new functionalized host molecules. Pure and Applied Chemistry,
1986. 58(11): p. 1523-1528.
PT

33. Seridi, L., A. Boufelfel, and S. Soltani, Structural, electronic and QTAIM analysis of host-
guest interaction of Warfarin with β-cyclodextrin and calix [4] arene. Journal of Molecular
Liquids, 2016. 221: p. 885-895.
CE

34. Yang, W. and M.M. de Villiers, Effect of 4-sulphonato-calix [n] arenes and cyclodextrins on
the solubilization of niclosamide, a poorly water soluble anthelmintic. The AAPS journal,
2005. 7(1): p. E241-E248.
35. Yang, W. and M.M. de Villiers, The solubilization of the poorly water soluble drug nifedipine
AC

by water soluble 4-sulphonic calix [n] arenes. European journal of pharmaceutics and
biopharmaceutics, 2004. 58(3): p. 629-636.
36. Millership, J.S., A preliminary investigation of the solution complexation of 4-sulphonic calix
[n] arenes with testosterone. Journal of inclusion phenomena and macrocyclic chemistry,
2001. 39(3-4): p. 327-331.
37. Galindo‐Murillo, R., L.E. Aguilar‐Suárez, and J. Barroso‐Flores, A mixed DFT‐MD
methodology for the in silico development of drug releasing macrocycles. Calix and thia‐calix
[N] arenes as carriers for Bosutinib and Sorafenib. Journal of computational chemistry,
2015.
38. Law, V., et al., DrugBank 4.0: shedding new light on drug metabolism. Nucleic acids
research, 2014. 42(D1): p. D1091-D1097.
39. Andreetti, G.D., R. Ungaro, and A. Pochini, Crystal and molecular structure of cyclo {quater
[(5-t-butyl-2-hydroxy-1, 3-phenylene) methylene]} toluene (1: 1) clathrate. Journal of the
Chemical Society, Chemical Communications, 1979(22): p. 1005-1007.

18
 ACCEPTED MANUSCRIPT

40. Coruzzi, M., et al., Molecular inclusion in functionalized macrocycles. Part 5. The crystal
and molecular structure of 25, 26, 27, 28, 29-pentahydroxycalix [5] arene–acetone (1: 2)
clathrate. Journal of the Chemical Society, Perkin Transactions 2, 1982(9): p. 1133-1138.
41. Halit, M., et al., Crystal and molecular structure of two calix [6] arenes: p-Isopropylcalix [6]
arene andp-tert-butylcalix [6] arene—benzene (1∶ 3) complex. Journal of inclusion
phenomena, 1988. 6(6): p. 613-623.
42. Gutsche, C.D., A.E. Gutsche, and A.I. Karaulov, Calixarenes 11. Crystal and molecular
structure ofp-tert-butylcalix [8] arene. Journal of inclusion phenomena, 1985. 3(4): p. 447-
451.
43. Allen, F.H., The Cambridge Structural Database: a quarter of a million crystal structures
and rising. Acta Crystallographica Section B: Structural Science, 2002. 58(3): p. 380-388.
44. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G.

PT
Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P.
Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K.
Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T.

RI
Vreven, J.A. Montgomery, J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N.
Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C.

SC
Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B.
Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J.
Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski,
G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Farkas, J.B. Foresman,
NU
J.V. Ortiz, J. Cioslowski, D.J. Fox, Gaussian 09, Revision B.01, Wallingford CT, 2009.
45. Grimme, S., Semiempirical GGA‐type density functional constructed with a long‐range
dispersion correction. Journal of computational chemistry, 2006. 27(15): p. 1787-1799.
46. Bernardino, R.J. and B.J.C. Cabral, Structure and conformational equilibrium of thiacalix [4]
MA

arene by density functional theory. Journal of Molecular Structure: THEOCHEM, 2001.

549(3): p. 253-260.
47. Athar, M., M.Y. Lone, and P.C. Jha, Investigation of structure and conformational
equilibrium of Oxacalix [4] arene: A density functional theory approach. Journal of
D

Molecular Liquids, 2017.

48. Version, A.D.S., 4.0, Accelrys, San Diego, USA.
E

49. Cheng, A. and K.M. Merz, Prediction of aqueous solubility of a diverse set of compounds
using quantitative structure− property relationships. Journal of medicinal chemistry, 2003.
PT

46(17): p. 3572-3580.
50. Egan, W.J. and G. Lauri, Prediction of intestinal permeability. Advanced drug delivery
reviews, 2002. 54(3): p. 273-289.
CE

51. Egan, W.J., K.M. Merz, and J.J. Baldwin, Prediction of drug absorption using multivariate
statistics. Journal of medicinal chemistry, 2000. 43(21): p. 3867-3877.
52. Susnow, R.G. and S.L. Dixon, Use of robust classification techniques for the prediction of
human cytochrome P450 2D6 inhibition. Journal of chemical information and computer
AC

sciences, 2003. 43(4): p. 1308-1315.

53. Xia, X., et al., Classification of kinase inhibitors using a Bayesian model. Journal of
medicinal chemistry, 2004. 47(18): p. 4463-4470.
54. Dixon, S.L. and K.M. Merz, One-dimensional molecular representations and similarity
calculations: methodology and validation. Journal of medicinal chemistry, 2001. 44(23): p.
3795-3809.
55. Votano, J.R., et al., QSAR Modeling of Human Serum Protein Binding with Several Modeling
Techniques Utilizing Structure− Information Representation. Journal of medicinal chemistry,
2006. 49(24): p. 7169-7181.
56. Schneidman-Duhovny, D., et al., PatchDock and SymmDock: servers for rigid and symmetric
docking. Nucleic acids research, 2005. 33(suppl 2): p. W363-W367.
57. Connolly, M.L., Analytical molecular surface calculation. Journal of Applied
Crystallography, 1983. 16(5): p. 548-558.

19
 ACCEPTED MANUSCRIPT

58. Zhang, C., et al., Determination of atomic desolvation energies from the structures of
crystallized proteins. Journal of molecular biology, 1997. 267(3): p. 707-726.
59. Mashiach, E., et al., FireDock: a web server for fast interaction refinement in molecular
docking. Nucleic acids research, 2008. 36(suppl 2): p. W229-W232.
60. Ritchie, D.W. and G.J. Kemp, Protein docking using spherical polar Fourier correlations.
Proteins: Structure, Function, and Bioinformatics, 2000. 39(2): p. 178-194.
61. Macindoe, G., et al., HexServer: an FFT-based protein docking server powered by graphics
processors. Nucleic acids research, 2010: p. gkq311.
62. Ritchie, D.W. and V. Venkatraman, Ultra-fast FFT protein docking on graphics processors.
Bioinformatics, 2010. 26(19): p. 2398-2405.
63. Kleinjung, J. and F. Fraternali, Design and application of implicit solvent models in
biomolecular simulations. Current opinion in structural biology, 2014. 25: p. 126-134.

PT
64. Chen, J., C.L. Brooks, and J. Khandogin, Recent advances in implicit solvent-based methods
for biomolecular simulations. Current Opinion in Structural Biology, 2008. 18(2): p. 140-148.
65. Onufriev, A., D. Bashford, and D.A. Case, Exploring protein native states and large‐scale

RI
conformational changes with a modified generalized born model. Proteins: Structure,
Function, and Bioinformatics, 2004. 55(2): p. 383-394.

SC
66. Vanommeslaeghe, K., et al., CHARMM general force field: A force field for drug‐like
molecules compatible with the CHARMM all‐atom additive biological force fields. Journal of
computational chemistry, 2010. 31(4): p. 671-690.
67. Wu, X., et al., A core-weighted fitting method for docking atomic structures into low-
NU
resolution maps: application to cryo-electron microscopy. Journal of structural biology, 2003.
141(1): p. 63-76.
68. Smith, J.C. and M. Karplus, Empirical force field study of geometries and conformational
transitions of some organic molecules. Journal of the American Chemical Society, 1992.
MA

114(3): p. 801-812.
69. MacKerell Jr, A.D., et al., All-atom empirical potential for molecular modeling and dynamics
studies of proteins. The journal of physical chemistry B, 1998. 102(18): p. 3586-3616.
70. van Duynhoven, J.P., et al., Control of calix [6] arene conformations by self-inclusion of 1, 3,
D

5-tri-O-alkyl substituents: synthesis and NMR studies. Journal of the American Chemical
Society, 1994. 116(13): p. 5814-5822.
E

71. Fischer, S., et al., Pathways for conformational interconversion of calix [4] arenes. Journal of
the American Chemical Society, 1995. 117(5): p. 1611-1620.
PT

72. Lee, M.S., F.R. Salsbury Jr, and C.L. Brooks III, Novel generalized Born methods. The
Journal of chemical physics, 2002. 116(24): p. 10606-10614.
73. Lee, M.S., et al., New analytic approximation to the standard molecular volume definition
CE

and its application to generalized Born calculations. Journal of computational chemistry,

2003. 24(11): p. 1348-1356.
74. Leeson, P.D. and B. Springthorpe, The influence of drug-like concepts on decision-making in
medicinal chemistry. Nature Reviews Drug Discovery, 2007. 6(11): p. 881-890.
AC

75. Athar, M., et al., Pharmacophore model prediction, 3D-QSAR and molecular docking studies
on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson
drug design. Journal of Biomolecular Structure and Dynamics, 2016. 34(6): p. 1282-1297.
76. Bickerton, G.R., et al., Quantifying the chemical beauty of drugs. Nature chemistry, 2012.
4(2): p. 90-98.
77. Danylyuk, O. and K. Suwinska, Solid-state interactions of calixarenes with biorelevant
molecules. Chemical Communications, 2009(39): p. 5799-5813.
78. Jun, S.W., et al., Preparation and characterization of simvastatin/hydroxypropyl-β-
cyclodextrin inclusion complex using supercritical antisolvent (SAS) process. European
Journal of Pharmaceutics and Biopharmaceutics, 2007. 66(3): p. 413-421.
79. Grimme, S., S. Ehrlich, and L. Goerigk, Effect of the damping function in dispersion
corrected density functional theory. Journal of computational chemistry, 2011. 32(7): p. 1456-
1465.

20
 ACCEPTED MANUSCRIPT

80. Lengauer, T. and M. Rarey, Computational methods for biomolecular docking. Current
opinion in structural biology, 1996. 6(3): p. 402-406.
81. Alvira, E., J. Mayoral, and J. Garcia, Molecular modelling study of β-cyclodextrin inclusion
complexes. Chemical physics letters, 1997. 271(1-3): p. 178-184.
82. Bodor, N., M.-J. Huang, and J.D. Watts. Theoretical am1 studies of inclusion complexes of α-
and β-cyclodextrins with methylated benzoic acids and phenol, and γ-cyclodextrin with
buckminsterfullerene. in Proceedings of the Eighth International Symposium on
Cyclodextrins. 1996. Springer.
83. Huang, M.J., J.D. Watts, and N. Bodor, Theoretical studies of inclusion complexes of
β‐cyclodextrin with methylated benzoic acids. International journal of quantum chemistry,
1997. 64(6): p. 711-719.
84. Schneidman‐Duhovny, D., et al., Taking geometry to its edge: fast unbound rigid (and

PT
hinge‐bent) docking. Proteins: Structure, Function, and Bioinformatics, 2003. 52(1): p. 107-
112.
85. Dupont, N., et al., Solid state structures of the complexes between the antiseptic chlorhexidine

RI
and three anionic derivatives of calix [4] arene. CrystEngComm, 2008. 10(8): p. 975-977.
86. Ordaz, J.C., et al., Possibility of a magnetic [BN fullerene: B 6 cluster]− nanocomposite as a

SC
vehicle for the delivery of dapsone. New Journal of Chemistry, 2017. 41(16): p. 8045-8052.
87. Desiraju, G.R., Chemistry beyond the molecule. Nature, 2001. 412(6845): p. 397-400.
NU
MA
E D
PT
CE
AC

21
 ACCEPTED MANUSCRIPT

PT
RI
SC
NU
MA
D
E
PT

Graphical abstract
CE
AC

22
 ACCEPTED MANUSCRIPT

Highlights
 Calixarene based drug carriers for three tyrosine kinase inhibitors were proposed.
 Interaction energy of inclusion complexes were computed via computational methods.
 A range of binding mode can be possible for the drug-calixarene complexes.
 Dominance of interaction type depends upon the structural configuration.

PT
RI
SC
NU
MA
E D
PT
CE
AC

23