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Molecular docking studies of some topoisomerase II inhibitors: Implications in designing of novel anticancer drugs
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ScienceDirect Radiology of Infectious Diseases 6 (2019) 68e79 www.elsevier.com/locate/jrid
Research Article
Molecular docking studies of some topoisomerase II inhibitors: Implications in designing of novel anticancer drugs David Ebuka Arthur Department of Chemistry, Ahmadu Bello University Zaria, Kaduna State, Nigeria Received 13 March 2019; revised 12 June 2019; accepted 19 June 2019 Available online 23 July 2019
Abstract Objective: This study entails the structure-based design of type II inhibitors of human topoisomerase, by some notable anticancer compounds registered in the National Cancer Institute (NCI). The study aims to identify a series of more potent Top II inhibitors but are resistant to biochemical interaction with BRCA1 enzyme responsible for identifying and removing damaged cells resulting from a mutagenic response and finally subjecting the identified lead compound in the design of more active drug candidates. Methods: The structure-based drug design technique employed was molecular docking and the ICM pro software was used in both the preparation of the receptor and the docking process. The results were presented in both 2-dimensional and 3-dimensional views to best capture the binding poses as well as their interaction with the amino acids present in the binding pockets. Results: The result of our molecular docking study showed that Rubidazone and other ligands such as DAUNORUBICIN, m-AMSA, BISANTRENE HCl and MITOXANTRONE with binding score for topoisomerase given as 32.894e2.7452, 26.231, 25.022 and 25.843 respectively, were the best topoisomerase II inhibitors. VP-16 was selected as the lead compound, which was then utilized in designing new and improving topoisomerase II inhibitors by introducing one or more secondary functional groups containing heteroatoms. Conclusion: Our findings suggested that the presence of p- p, p -sigma and p-alkyl interactions of all the strategies with the receptor were primarily responsible for its firm ternary complex with topoisomerase o-DNA complex. © 2019 Beijing You’an Hospital affiliated to Capital Medical University. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Keywords: Topoisomerase II inhibitors; Etoposide; Intercalation; Pi-alkyl interaction
1. Introduction Cancer is a life-threatening disease that affects people from all parts of the world. A total of 7.6 million people were estimated to have died due to cancer worldwide in the year 2008 alone [12]. Other scientist have estimated that the global cancer burden will increase to 27 million new cases by 2050 [13]). In the previous years, the usage of numerous chemotherapy drugs has resulted in the positive treatment of several types of cancers. A few of the well-known chemotherapy drugs are E-mail address: [email protected]. Peer review under responsibility of Beijing You'an Hospital affiliated to Capital Medical University.
briefly described as Antimetabolites, Genotoxic Drugs, Alkylating agents and Intercalating agents, which are drugs that organize themselves by filling up spaces that are present within the nucleotides in the double helix DNA. They function by interfering with the processes such as transcription, replication and induce mutations. Examples are Doxorubicin, Idarubicin [11] (see Figs. 1 and 2). The identification of topoisomerase in the late twentieth century, led to the explosion of interest in topoisomerase and the advancement of chemicals that can specifically hinder this receptor. Topoisomerase assume an immediate integral part in the usual DNA stands replication. Topoisomerase assist this technique through a reversible trans-esterification reaction, this produces a covalent complex that is formed when the
https://doi.org/10.1016/j.jrid.2019.06.003 2352-6211/© 2019 Beijing You’an Hospital affiliated to Capital Medical University. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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Fig. 1. 3D view of Rubidazone-DNA complex in Topoisomerase II inhibition.
Fig. 2. (a) 3D view of Daunorubicin-DNA complex in Topoisomerase II inhibition, (b) 3D view of VP-16-DNA complex in Topoisomerase II inhibition.
tyrosine part of the compound is bound with the end of 30 phosphotyrosine in a DNA strand. BRCA1 is a fragment of enzyme complex that repairs DNA when both strands are damaged, it interacts with the DNA mismatch repair protein MSH2 [20]. BRCA binds directly to a DNA, but the complexity of branched DNA structures has been reported to significantly increase their interaction. This ability of BRCA to bind to DNA adds to its capacity to constrain the nuclease activity of the MRN complex in addition to the nuclease activity of Mre11 alone [17]. This could be
responsible for the part for BRCA1 in promoting lower conformity DNA repair by Non-Homologous End Joining (NHEJ). Computational methods are useful in making decisions and mimic virtually every aspect of drug discovery and development [14]. For example, in the hit identification phase in which drug discovery teams are provided with many novel chemicals to test for several potential lead molecules that possess the desired drug properties, in silico method of drug discovery would be an ideal method to use [7].
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Table 1 Structure, Name, CAS and NSC number of the complete dataset. Structure
Name
CAS
NSC number
AMONAFIDE
69408-81-7
308847
ANTHRAPYRAZOLE
91440-30-1
355644
BISANTRENE HYDROCHLORIDE
71439684
337766
DAUNORUBICIN
23541-50-6
82151
DEOXEODOXORUBIC-IN
63950-06-1
267469
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Table 1 (continued ) Structure
Name
CAS
NSC number
DOXORUBICIN HYDROCHLORIDE
25316-40-9
357704
m-AMSA (AMSACRINE)
51264-14-3
249992
MENOGARIL
71628-96-1
269148
MITOXANTRON
70476-82-3
301739
VP-16 (ETOPOISOMERASE OSIDE)
33419-42-0
141540
(continued on next page)
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Table 1 (continued ) Structure
Name
CAS
NSC number
RUBIDAZONE
36508-71-1
164011
PYRAZOLOACRIDINE
99009-21-9
366140
OXANTHRAZOLE
105118-12-5
349174
N,N-DIBENZYLDAUNORUBICIN
70878-51-2
268242
Table 2 Molecular docking score of some compound against Human topoisomerase. Title
Entry ID
Score
Nflexi
H-bond
H-phob
VwInt
Eintl
Dsolv
SolEl
AMONAFIDE ANTHRAPYRAZOLE DERIVATIVE BISANTRENE HCl DAUNORUBICIN deoxydoxorubicin DOXORUBICIN m-AMSA MENOGARIL MITOXANTRONE N,N-DIMENZYL DAUNOMYCIN OXANTHRAZOLE PYRAZOLOACRIDINE RUBIDAZONE VP-16
1 2 3 4 5 6 7 8 9 10 11 12 13 14
17.209 19.316 25.022 27.457 24.799 22.58 26.231 17.931 25.843 23.86 21.875 22.225 32.469 23.015
3 9 2 6 7 8 2 5 12 10 10 5 7 5
0.936 5.023 2.24 7.637 4.08 6.685 0 1.41 6.999 3.576 3.675 0 6.438 1.126
3.545 5.068 4.987 5.255 4.719 4.824 5.328 6.259 5.028 7.602 4.988 5.545 6.614 6.131
26.415 29.899 33.589 32.454 35.598 32.331 31.301 29.305 33.272 41.38 34.535 31.234 41.175 36.182
1.781 9.075 3.122 9.511 4.074 15.135 6.801 0 5.1 10.543 7.267 3.138 13.533 5.267
12.268 21.187 16.795 22.108 21.586 26.217 9.327 16.605 20.027 21.617 19.897 10.853 24.41 19.898
4.467 8.177 5.726 11.605 5.898 8.232 0.673 5.579 9.523 14.316 6.634 2.401 10.482 3.332
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Table 3 Molecular docking result of some compound against BRCA1 protein. Title
Entry ID
Score
Nflex
Hbond
Hphob
VwInt
Eintl
Dsolv
SolEl
AMONAFIDE ANTHRAPYRAZOLE DERIVATIVE BISANTRENE HCl DAUNORUBICIN deoxydoxorubicin DOXORUBICIN m-AMSA MENOGARIL MITOXANTRONE N,N-DIMENZYL DAUNOMYCIN OXANTHRAZOLE PYRAZOLOACRIDINE RUBIDAZONE VP-16
1 2 3 4 5 6 7 8 9 10 11 12 13 15
9.174 10.586 12.295 5.527 9.478 9.672 15.821 12.233 1.845 16.859 5.887 3.387 18.619 7.889
3 9 2 6 7 8 2 5 12 10 10 5 7 5
0.445 2.699 1.204 2.818 3.62 5.637 0.915 4.169 3.427 3.312 1.413 0 3.869 2.229
4.895 6.223 6.678 6.258 6.139 6.081 5.441 6.03 5.639 9.194 5.545 5.938 8.862 7.163
10.459 26.374 25.939 27.813 27.925 28.075 24.888 19.412 24.981 40.381 26.245 22.073 40.526 22.084
5.577 3.885 10.775 16.671 10.972 20.433 6.313 0 9.182 25.929 6.534 5.933 27.932 14.684
13.096 11.968 11.725 15.82 18.695 22.5 6.175 16.258 19.899 14.572 19.078 7.993 19.24 14.261
18.814 18.802 16.926 27.489 20.451 22.823 13.934 9.961 20.393 32.02 28.958 30.976 28.794 16.57
Nflex:- Number of Rotatable torsions, Hbond:- Hydrogen Bond energy, Hphob:- Hydrophobic Energy in exposing a surface to water, Vwint:- The Vander Waals Interaction Energy (sum of gc and gh Vander Waals), Eintl:- Internal Conformational Energy of the ligand, Dsolv:- The desolvation of exposed H-bond donors and acceptors, SolEl:- The solvation electrostatics energy change upon binding.
2. Experimental section The equipment and programming utilized in this study and the computational analysis such as for chemical structure optimization, dynamics and docking study incorporates: Computer (HP Intel(R) core i5-4200U with 1.63 Hz and 2.3 Hz processor and windows 8.1), wavefunction Spartan 14.1.4 [10], ChemBio Ultra 12.0 [9,16], Molsoft v3.8.3 software [1,2]. 3. Ligand preparation The 2D structure of each Topoisomerase II inhibitor [3,4] were downloaded as mol files from the chemical book website (http://www.chemicalbook.com/) using their chemical abstract service (CAS) number as presented in Table 1. The structures were introduced into wavefunction 14 graphic user interphase (GUI) after which the 2D structures were converted
into 3D structure by selecting the view dialog box present on Spartan 14 GUI. From the built option on Spartan 14 the structures were cleaned by checking minimize using molecular mechanic force field (MMþ) option in order to remove all strain from the molecular structure. In addition this will ensure a well defined conformer relationship among compounds of the study [19]. From the set up calculation option on Spartan 14, the calculation was set to equilibrium geometry at the ground state using density functional theory at B3LYP (Becke 88 three-parameter hybrid exchange potentials with Lee-YangParr correlation potential) level of theory and 6-311G (d) basis set for the geometrical optimization of the cleansed structures i.e. B3LYP/6-311G (d) level of theory. 4. Preparation of receptor The x-ray diffraction structure of Human topoisomerase II beta with PDB ID: 3QX3 [22] with a resolution 2.16 Å was
Fig. 3. (a) 3D view of VP-16 (8A)-DNA complex in Topoisomerase II inhibition, (b) 3D view of VP-16 (6A)-DNA complex in Topoisomerase inhibition.
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Table 4 VP 16 Derivatives docking results on Human topoisomerase. Entry ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
Term VP-16 8A VP-16 6B VP-16 9A VP-16 8B VP-16 8C VP-16 6A VP-16 9C VP-16 5A VP-16 9B VP-16 7C VP-16 6C VP-16 10A VP-16 4A VP-16 5C VP-16 5B VP-16 7A VP-16 3C VP-16 10B VP-16 10C VP-16 7B VP-16 2A VP-16 1C VP-16 3A VP-16 2C VP-16 2B VP-16 4B VP-16 4C VP-16 3B VP-16 1B VP-16 1A
Score 31.944 31.003 30.775 30.163 30.012 29.797 29.51 28.619 28.388 28.21 27.784 27.482 27.307 26.832 26.768 26.678 26.616 26.323 26.307 25.916 25.34 24.349 24.318 23.986 23.669 23.22 23.044 22.846 20.506 17.04
kI
N-flex
H-bond
H-phob
V-wInt
E-intl
D-solv
SolEl
0.947 0.949 0.949 0.95 0.951 0.951 0.951 0.953 0.953 0.953 0.954 0.955 0.955 0.956 0.956 0.956 0.956 0.957 0.957 0.957 0.958 0.96 0.96 0.96 0.961 0.962 0.962 0.962 0.966 0.972
7 5 8 6 6 7 7 8 7 7 5 6 6 5 5 7 6 6 6 7 6 6 7 5 5 7 7 6 5 5
4.065 4.489 4.049 2.881 2.89 2.962 4.206 2.819 2.895 5.445 2.239 3.347 3.344 2.24 2.259 2.688 2.205 1.805 2.647 2.472 2.888 1.67 1.152 2.648 3.857 1.063 1.12 1.056 1.714 0.797
7.195 6.182 6.704 7.332 7.26 7.409 7.394 6.938 6.88 6.148 6.344 6.027 6.033 6.238 6.247 7.593 6.774 5.989 6.476 6.585 5.58 5.611 6.471 5.41 5.923 6.18 5.677 6.657 6.298 6.277
47.006 38.023 46.782 43.881 43.588 47.958 45.132 45.848 42.978 36.927 38.823 42.997 43.141 39.333 39.343 48.2 38.668 43.033 43.974 40.631 42.821 44.539 43.046 38.779 41.154 38.237 35.619 38.868 37.888 40.121
16.952 10.08 15.253 10.102 8.804 12.707 21.093 16.194 9.401 11.728 8.956 8.749 7.913 8.731 8.264 19.272 10.269 9.118 9.242 12.78 10.284 11.176 8.894 6.97 17.341 6.319 8.544 7.923 9.135 13.95
28.131 21.93 28.451 24.233 24.06 25.628 27.485 23.32 24.624 24.619 20.83 24.872 26.373 21.524 22.076 29.687 21.2 22.532 26.212 23.066 23.613 24.978 23.028 23.439 29.213 20.046 16.696 21.961 23.286 27.501
7.376 4.655 6.977 6.281 6.225 10.908 9.703 10.181 5.84 5.982 3.531 8.739 7.512 4.855 4.423 10.524 4.045 7.257 8.249 5.883 10.934 8.85 6.829 6.874 9.549 3.958 3.774 4.672 8.294 8.602
used for the study. The complexed Etoposide inhibitor was removed from the B-side of 3QX3 where it was covalently bonded with the DNA in the receptor. The receptor structure was imported into the Molsoft.icmpro.v3.8.3 GUI [1,2], and the PDB files was converted into
an ICM-object by removing the additional water molecules confined in the x-ray structure collected from PDB data bank. All the hydrogen atoms were optimized and while some other amino acids such as Histidine, proline, glycine, cysteine etc, which were missing as well as other missing side chains were also treated before the receptor was then applied through the process of molecular docking treatment. 5. Docking method
Fig. 4. 3D view of VP-16 (9A)-DNA complex in Topoisomerase inhibition.
The Human topoisomerase II beta after treatment was docked with the ligands, five types of interaction potentials that represent the receptor pocket including van der Waals potential for a hydrogen atom probe, van der Waals potential for a heavy-atom probe (generic carbon of 1.7A radius), optimizing electrostatic term, hydrophobic terms and loan-pair-based potential, which reflected directional preferences in hydrogen bonding. These energy terms were based on the all-atom vacuum force field ECEPP/3 with added functions to account for solvation free energy and entropic contribution. The conformational sampling in the programme was based on the biased probability Monte Carlo (BPMC) procedure, which randomly selected a conformation in the internal coordinate space and then made a step to a new random position independent of the previous one but according to a predefined continuous probability distribution. It was shown that after each random step, full local minimization
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Table 5 VP 16 Derivatives docking score on BRCA1 protein. Entry ID
Term
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16
10C 10B 10A 9C 9B 9A 8C 8B 8A 7C 7B 7A 6C 6B 6A 5C 5B 5A 4C 4B 4A 3C 3B 3A 2C 2B 2A 1C 1B 1A
Score
KI
H-phob
V-wInt
E-intl
D-solv
SolEl
6.128 9.816 5.924 7.628 8.065 13.641 4.055 12.306 7.971 0.170 5.290 11.117 14.131 12.791 15.720 1.161 16.442 11.938 10.893 9.339 7.810 17.354 5.716 2.851 4.767 8.650 7.016 4.351 6.828 1.971
0.990 0.984 0.990 0.987 0.986 0.977 0.993 0.979 0.987 1.000 0.991 0.981 0.976 0.979 0.974 0.998 0.973 0.980 0.982 0.984 0.987 0.971 0.990 0.995 0.992 0.985 0.988 0.993 0.989 0.997
7.756 8.422 8.742 9.287 9.355 8.769 9.230 9.031 10.013 10.389 8.315 8.218 9.393 8.201 8.123 9.682 7.831 7.620 9.936 7.993 8.091 9.527 8.256 9.047 7.859 6.559 6.635 8.803 7.441 7.656
33.122 27.770 31.508 30.746 32.536 29.674 39.101 27.590 34.647 27.020 26.582 29.760 38.969 34.186 34.250 34.772 36.052 33.267 35.199 29.906 24.559 33.956 20.519 25.270 34.848 26.341 24.382 29.367 29.829 21.715
31.013 32.415 26.422 20.032 30.635 21.018 17.048 22.755 23.981 26.772 16.089 28.597 26.207 14.266 15.624 17.822 36.503 23.692 32.611 20.693 12.026 35.092 9.395 33.888 17.595 13.129 11.217 19.167 23.558 12.411
20.670 13.091 18.067 15.247 15.531 14.326 22.094 14.535 17.398 16.369 17.890 16.039 21.924 18.694 18.923 21.762 20.142 18.134 14.519 15.245 13.643 14.986 15.094 14.273 22.141 13.547 19.647 16.372 17.024 15.263
27.778 22.288 27.280 28.063 30.113 17.947 35.439 17.747 28.884 30.338 19.083 23.352 20.147 29.879 28.462 34.920 25.816 28.234 30.401 20.974 16.735 27.648 11.981 29.269 32.175 19.765 18.015 29.370 27.125 19.756
Table 6 Hydrogen and Hydrophobic bond interaction between some ligands and the receptor. Term
Hydrogen Bond (HB) interaction
Bond Length (Å) for HB interaction
Hydrophobic interaction
Rubidazone Daunorubicin m-AMSA Mitoxanthrone Bisantrene HCl VP-16
Dt15, Dc14, Dg13, Da6, Dg7 Dc14, Dt15, Da6, Dg7, Dc8 Dc8 Dc8, Da6 Dg13 Dg13
3.06, 2.74, 2.98 2.65, 3.23, 3.07
Dg5, Da12, Dc8, Dt9 Da12, Dt9, dg13, Dg5 Dt9, Da12, Dg13 Dt9, Da12, Dg13, Dg7, Dc14, Dg5 Da12, Dc8, Dc14 Da12, Dc8, Dt9, Dg10
2.72, 3.25, 2.79, 2.77 3.06, 2.79, 3.85, 3.03 (2.95, 2.73) 2.78
greatly improved the efficiency of the procedure. The ICM program relied on global optimization of the entire flexible ligand in the receptor field and combined large-scale random moves of several types with gradient local minimization and a search history mechanism.
polar solvation energy differences between bound and unbound states, (v) electrostatic energy, (vi) hydrophobic energy, and (vii) hydrogen bond donor or acceptor desolvation. The lower the ICM score, the higher the chance the ligand was a binder.
6. Virtual screening - scoring
7. Designing topoisomerase II inhibitor
The scoring function was used to give a good approximation of the binding free energy between a ligand and a receptor, which was usually a function of different energy terms based on a force-field. The ICM scoring function was weighted according to the following parameters (i) internal force-field energy of the ligand, (ii) entropy loss of the ligand between bound and unbound states, (iii) ligandreceptor hydrogen bond interactions, (iv) polar and non-
The outcome of the ligands docked on Human topoisomerase II beta target was appraised and the interactions of best inhibitors were studied. The bulky side groups and other molecular descriptors presented in the lead compounds were altered to improve on their lethal effect on the cancer cells. This was made successful by incorporating some fragments found to bind intensely with the binding site of the receptor when docked with the same ICM-pro Molsoft program.
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Fig. 5. 3D view of VP-16 (6A)- BRCA1 complex and 2D interaction of VP-16 6A interaction at the binding site.
Table 7 Hydrogen and Hydrophobic bond interaction between the best newly designed ligands and the receptor (Topoisomerase). Term VP-16 VP-16 VP-16 VP-16 VP-16 VP-16
(8A) (6B) (9A) (8B) (8C) (6A)
Hydrogen Bond (HB) interaction
Bond Length (Å) for HB interaction
Hydrophobic interaction
Dg10, Dg10, Dg10, Dg10, Dg10, Dg10,
3.04, 3.15 (2.89, 2.89), (3.18, 3.30) 2.95, 3.16 2.95, 3.10 2.96, 3.10 2.92, 2.94
Dc8, Dt9, Da12, Dc11, Dc8, Dt9, Da12 Dc11, Da12, Dc8, Dt9 Dc11, Da12, Dc8, Dt9 Dc11, Dc8, Dt9, Da12 Dc11, Da12, Dc8, Dt9
Dg13 Dg13 Dg13 Dg13 Dg13 Dg13
8. Validating new drugs for side reaction The newly designed drugs were also studied using molecular docking simulations to investigate their interaction with BRCA1 protein theoretically, the method for this quest was achieved by docking all the compound against the x-ray diffraction Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide PDB ID: 4Y2G [23] with a resolution 2.5 Å gotten from http://www.rcsb.org/. 9. Results and discussion for ligand-receptor docking The ligand-protein docking study done between the receptor topoisomerase and the inhibitors was presented in Table 2. All ligands docking pose were analyzed, they inhibit topoisomerase by intercalating the DNA and thereby inhibiting topoisomerase in the process. In the figures, we realized
that the ligands inhibition mechanisms were found to follow in both hydrophobic and hydrogen bonding interactions with the receptors understudy. Also, the strength of the inhibitors interaction with the receptors were a reflection on the frequency of hydrogen bonds appearing between the ligandprotein complex as shown in Table 2. The result showed a correlation between the score, which was the binding affinity of the compounds reported as free energy of binding in kcal/mol, with the values of the hydrogen bonds, hydrophobic bonds and number of flexible torsions present in the compounds under study. Rubidazone reported with a binding score of 32.469 kcal/ mol was found to have the highest binding affinity; its affinity for the binding site was largely as connected to the value of the hydrogen bond and hydrophobic bond energy, which was reported as 6.438 and 6.614 respectively. The molecular docking study of this ligand, when compared to VP-16 shows the
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Table 8 Hydrogen and Hydrophobic bond interaction between the best newly designed ligands and the receptor (BRCA1). Term
Hydrogen Bond (HB) interaction
Bond Length (Å) for HB interaction
Hydrophobic interaction
Pi-sigma, Amide interaction
Alkyl/PieAlkyl Interaction
Carbon-Hydrogen Interaction
VP-16 (3C)
Leu 1657, Sep406, Ser 404
(2.68, 2.80), (3.15, 3.09), 2.78
Arg 405
Pro 1659, Val 1654, Phe 1662, Tyr1662, Lys 1702, Leu 1701, Leu 1679
Asn 1678, Sep406
VP-16 (5B)
Leu 1657, Sep406, Ser 404, Asn 1678
2.74, (3.12, 3.17), 3.29, 2.77
e
Val 1654, Leu 1701, Leu 1679
Arg 405, Lys 1702
VP-16 (6A)
Leu 1657, Sep406, Ser 404
(3.08, 2.96), 3.20, 3.11, 2.87
Arg 405
Pro 1659, Phe 1662, Leu 1679, Val 1654
Asn 1678, Lys 1702
VP-16 (6C)
Asn 1678, Ser 404
2.97, 1.89
Phe 1662
Leu 1701, Leu 1679, Ile 1680
Pro 407, Arg 405, Leu 1657, Tyr403
VP-16 (9A)
Ser 404, Sep406
2.06, 2.35
Arg 405
Leu 1679, Leu 1701, Tyr403, Pro 1659
Leu 1657, Lys 1702, Asn 1678
VP-16 (9B)
Sep406, Ser 404
(2.91, 3.16, 3.17), 3.10
Val 1654, Phe 1662, Tyr1666, Arg 405, Gly 1656, Ser 1655, tyr403, Lys 1702, Pro 407, Asn 1678, Leu 1679 Phe 1662, Val 1654, Pro 1659, Leu 1679, Pro 407, Lys 1702, Tyr403, Arg 405 Pro 1659, Phe 1662, Val 1654, Lys 1702, Tyr403, Lys 1702, thr1658, Arg 405, Asn 1678, Lue 1679 Ser 404, Pro 407, Lue 1701, Ile 1680, Leu 1679, Sep 406, Arg 405, Leu 1657, Tyr403, Asn 1678, Pro 1659 Pro 407, Lys 1702, Asn 1678, Leu 1679, Arg 405, Leu 1657, Pro 1659, Phe 1662, Tyr403 Pro 407, Leu 1679, Lys 1702, Arg 405, Tyr403, Leu 1657, Phe 1662, Val 1654, Pro 1659
Arg 405
Phe 1662, Val 1654, Leu 1679, Pro 1659
Leu 1657
Fig. 6. 3D view of VP-16 (9A)- BRCA1 complex and 2D interaction of VP-16 9A interaction at the binding site.
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relevance of some secondary pharmacophore responsible for the interaction involving hydrogen bond-type between the ligands and sugar bases in a human DNA. Other ligands such as DAUNORUBICIN, m-AMSA, BISANTRENE HCl and MITOXANTRONE with binding score for topoisomerase given as 2.7452, 26.231, 25.022 and 25.843 respectively, were reported as the best topoisomerase II inhibitors when ranking their binding score for the most active on Table 2. These ligands were also docked against the enzyme BRCA1 that was a human tumor suppressor enzyme, the binding affinity of the compounds were all less than 20 kcal/ mol, indicating that they were not toxic to the tumor suppressor genes. VP-16 was found to have a low binding score of 7.889 as compared to other ligands that inhibited topoisomerase to a greater extent, such as Rubidazone (18.619), m-AMSA (15.821) and Bisantrene (12.295). The high binding affinity of VP-16 to topoisomerase and low affinity for BRCA1, suggesting that VP-16, though not as active when compared to other ligands, was much less toxic and providing promising opportunities in the designing of new topoisomerase II inhibitor, that was safer to the human body [5,8,15] (see Table 6). The newly designed VP-16 derivatives were docked on topoisomerase and its result reported in Table 7, the result showed that VP-16 (8A) had the highest binding affinity for the receptor, the binding energy (31.944 kcal/mol) placed the ligand as the most active topoisomerase II inhibitor studied here. The number of flexible bonds on the compound was the same as that for the lead compound, suggesting that the improved activity was not a function of the number of flexible torsions but a function of the added secondary pharmacophore responsible for significantly increasing its H-bond at the active site of the receptor. VP-16 (8A) bound to the receptor through hydrogen bond interaction with Dg10 (3.04) and Dg13 (3.15), while the hydrophobic interaction was with Dt8, Da12, Dc8 and Dc11 as seen in Fig. 3. Fig. 3 showed the presence of (pp) areneearene interactions between the ligand and the receptor, this interaction as reported by staker [18], were largely responsible for stabilizing the intercalation of VP-16 (8A) to the DNA-topoisomerase complex (see Fig. 4) (see Table 3). The molecular docking result of the receptoreligand complex for VP-16 (6A), revealed that VP-16 (6A) inserted at the position of DNA cleavage and its binding mechanism was like that of VP-16 (6B). An analysis of VP-16 (6A) complex proved that both ionic forms of the analogues present in the complex was instrumental to their improved binding affinity when compared with VP-16. The binding energy of the VP-16 (6A) to the enzyme topoisomerase was shown in Table 4 was reported as 29.797 kcal/mol. The number of rotatable torsions in the ligand was seven (7) signifying a lot of possible conformational structures within the binding site [6]. The presence of p-p interaction in the analogue with Dc11, Da12, Dc8 and Dt9 confirmed the stable pose of the ligand in the binding pocket. The hydrogen bond present between the hydroxyl group (OH-group) of the ring with Dg10 and Dg13 further contributeed to the high binding score of VP-16 (6A) to the topoisomerase receptor.
VP-16 (9A) inhibited Topoisomerase with a binding energy of 30.775 kcal/mol, the bulk of this energy contribution was from the Vander Waals interaction and hydrophobic energy (43.881 and 6.704 and respectively), while the hydrogen energy (H-bond energy) was given as 4.094. VP-16 (9A) intercalateed with DNA to inhibit the topoisomerase enzyme, by forming many areneearene (p-p) interaction with Dc11, Da12, Dc8 and Dt9, this p-p interaction stabilizes the VP-16 analogue [21]. While the presence of alkoxy-group on VP16(9A) increaseed its binding affinity by forming hydrogen bonds with surrounding Dg10 and Dg13 and the corresponding bond lengths (2.95)Å and 3.16 Å respectively as shown in Fig. 3(b), confirming the relationship between the binding affinity and the alkoxy group present in analogue VP-16(9A). All analogues of VP-16 drug bound to the protein BRCA1 satisfactorily, though their reported binding affinity presented in Table 5, which was reported to be low with values ranging from 0.170 to 17.351. It showed that the newly designed derivatives of VP-16 could be used as preferred substitute for the other topoisomerase II inhibitors studied in this work. The interactions of VP-16(A) captured in Fig. 5, indicated the presence of an amide pi stacked interaction with Arg 405, hydrogen bond interaction with Leu 1657, Sep406, Ser 404 with the corresponding bond lengths of (3.08, 2.96), 3.20, 3.11, 2.87, piealkyl interaction with Pro 1659, Phe 1662, Leu 1679, Val 1654 and finally a carbon-hydrogen bond type with Asn 1678, Lys 1702 were responsible for its stability. Other noticeable analogue such as VP-16(9A) interactions with BRCA1 were also presented in Table 8, its 2D interaction was shown in Fig 6. More than 10 interaction contacts were noticed within the complex binding site and this could be attributed to the large flexible bonds in VP-16(9A). These results were promising and superior to other Topoisomerase II inhibitors docking results carried out within this study, and hence making VP-16(8A, 8B and 6A) the most active and less toxic topoisomerase II inhibitor . 10. Conclusion The docking study done amid at the target Topoisomerase (PDB: 3QX3) and the studied inhibitors were found to be successfully completed using a molsoft program. The inhibitors were found to prevent the enzyme from completing their primary function by wholly lodging the active sites in the intended receptor; the mechanism for this reaction was the same in all cases, which took into account of the ligands intercalated through covalently joined Topoisomerase-DNA complex. The compounds with the highest binding affinity for the enzyme was employed, to design new analogues, thus successfully enhancing the bioactivity of the lead compound. VP-16 analogues designed considerably different in bioactivity from the lead compound since by addition of heterocontaining groups, as well as other highly electronegative elements such as the halide groups, were responsible for enhancing the binding energy of the ligand. This was evident when the number of hydrogen bonds interaction present in the complex were increased. In conclusion, our research proposed
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a better anticancer drug, which was computationally validated and were found to be more potent, less toxic when used as topoisomerase oisomerase II inhibitors. VP-16 (8A) through the binding energy of 39.144 kcal/mol was confirmed to be the best inhibitor, since its binding energy, when entangled with topoisomerase oisomerase, far surpassed other ligands that were studied. Therefore, we hope that future studies, would take into account of the synthesis and experimental validation of this novel analogues clearly accessible in this manuscript in order to affirm our theory. References [1] Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235(3):983e1002. [2] An J, Totrov M, Abagyan R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteom 2005; 4(6):752e61. [3] Arthur DE, Uzairu A, Mamza P, Abechi E, Shallangwa G. Qsar modelling of some anticancer PGI50 activity on hl-60 cell lines. Albanian J Pharm Sci 2016;3(1):4e9. [4] Arthur DE, Uzairu A, Mamza P, Abechi S. Quantitative structureeactivity relationship study on potent anticancer compounds against MOLT-4 and P388 leukemia cell lines. J Adv Res 2016;7(5):823e37. [5] Chen L, Chen X. Results of molecular docking as descriptors to predict human serum albumin binding affinity. J Mol Graph Model 2012;33:35e43. [6] Cremer Dt, Pople J. General definition of ring puckering coordinates. J Am Chem Soc 1975;97(6):1354e8. [7] Damme SV, Bultinck P. A new computer program for QSAR-analysis: ARTE-QSAR. J Comput Chem 2007;28(11):1924e8. [8] Davis GDJ, Vasanthi AHR. QSAR based docking studies of marine algal anticancer compounds as inhibitors of protein kinase B (PKBb). Eur J Pharm Sci 2015;76:110e8. [9] Evans DA. History of the harvard ChemDraw project. Angew Chem Int Ed 2014;53(42):11140e5. [10] Hehre WJ, Huang WW. Chemistry with computation: an introduction to SPARTAN. Wavefunction, Inc; 1995. [11] Herrlich P, Morrison H, Sleeman J, ORIAN-ROUSSEAU V, K€onig H, WEG-REMERS S, et al. CD44 acts both as a growth-and invasivenesspromoting molecule and as a tumor-suppressing cofactor. Ann N Y Acad Sci 2000;910(1):106e20.
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[12] Hirpara KV, Aggarwal P, Mukherjee AJ, Joshi N, Burman AC. Quercetin and its derivatives: synthesis, pharmacological uses with special emphasis on anti-tumor properties and prodrug with enhanced bio-availability. Anti Cancer Agents Med Chem 2009;9(2): 138e61. [13] Keelan J, Pavri-Garcia V, Tomlinson G, Wilson K. YouTube as a source of information on immunization: a content analysis. JAMA 2007; 298(21):2482e4. [14] Khandelwal A, Bahadduri PM, Chang C, Polli JE, Swaan PW, Ekins S. Computational models to assign biopharmaceutics drug disposition classification from molecular structure. Pharm Res 2007;24(12): 2249e62. [15] Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 2004;3(11):935. [16] Li Z, Wan H, Shi Y, Ouyang P. Personal experience with four kinds of chemical structure drawing software: review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch. J Chem Inf Comput Sci 2004; 44(5):1886e90. [17] Paull TT, Cortez D, Bowers B, Elledge SJ, Gellert M. Direct DNA binding by Brca1. Proc Natl Acad Sci 2001;98(11):6086e91. [18] Staker BL, Feese MD, Cushman M, Pommier Y, Zembower D, Stewart L, et al. Structures of three classes of anticancer agents bound to the human topoisomerase I DNA covalent complex. J Med Chem 2005; 48(7):2336e45. [19] Viswanadhan VN, Ghose AK, Revankar GR, Robins RK. Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics. J Chem Inf Comput Sci 1989;29(3):163e72. [20] Warmoes M, Jaspers JE, Pham TV, Piersma SR, Oudgenoeg G, Massink MP, et al. Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with potential diagnostic and prognostic value in human breast cancer. Mol Cell Proteom 2012;11(7): 013334. M111. [21] Waters ML. Aromatic interactions in model systems. Curr Opin Chem Biol 2002;6(6):736e41. [22] Wu C-C, Li T-K, Farh L, Lin L-Y, Lin T-S, Yu Y-J, et al. Structural basis of type II topoisomerase inhibition by the anticancer drug etoposide. Science 2011;333(6041):459e62. [23] Wu Q, Paul A, Su D, Mehmood S, Foo TK, Ochi T, et al. Structure of BRCA1-BRCT/abraxas complex reveals phosphorylation-dependent BRCT dimerization at DNA damage sites. Mol Cell 2016;61(3): 434e48.
H O S T E D BY
ScienceDirect Radiology of Infectious Diseases 6 (2019) 68e79 www.elsevier.com/locate/jrid
Research Article
Molecular docking studies of some topoisomerase II inhibitors: Implications in designing of novel anticancer drugs David Ebuka Arthur Department of Chemistry, Ahmadu Bello University Zaria, Kaduna State, Nigeria Received 13 March 2019; revised 12 June 2019; accepted 19 June 2019 Available online 23 July 2019
Abstract Objective: This study entails the structure-based design of type II inhibitors of human topoisomerase, by some notable anticancer compounds registered in the National Cancer Institute (NCI). The study aims to identify a series of more potent Top II inhibitors but are resistant to biochemical interaction with BRCA1 enzyme responsible for identifying and removing damaged cells resulting from a mutagenic response and finally subjecting the identified lead compound in the design of more active drug candidates. Methods: The structure-based drug design technique employed was molecular docking and the ICM pro software was used in both the preparation of the receptor and the docking process. The results were presented in both 2-dimensional and 3-dimensional views to best capture the binding poses as well as their interaction with the amino acids present in the binding pockets. Results: The result of our molecular docking study showed that Rubidazone and other ligands such as DAUNORUBICIN, m-AMSA, BISANTRENE HCl and MITOXANTRONE with binding score for topoisomerase given as 32.894e2.7452, 26.231, 25.022 and 25.843 respectively, were the best topoisomerase II inhibitors. VP-16 was selected as the lead compound, which was then utilized in designing new and improving topoisomerase II inhibitors by introducing one or more secondary functional groups containing heteroatoms. Conclusion: Our findings suggested that the presence of p- p, p -sigma and p-alkyl interactions of all the strategies with the receptor were primarily responsible for its firm ternary complex with topoisomerase o-DNA complex. © 2019 Beijing You’an Hospital affiliated to Capital Medical University. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Keywords: Topoisomerase II inhibitors; Etoposide; Intercalation; Pi-alkyl interaction
1. Introduction Cancer is a life-threatening disease that affects people from all parts of the world. A total of 7.6 million people were estimated to have died due to cancer worldwide in the year 2008 alone [12]. Other scientist have estimated that the global cancer burden will increase to 27 million new cases by 2050 [13]). In the previous years, the usage of numerous chemotherapy drugs has resulted in the positive treatment of several types of cancers. A few of the well-known chemotherapy drugs are E-mail address: [email protected]. Peer review under responsibility of Beijing You'an Hospital affiliated to Capital Medical University.
briefly described as Antimetabolites, Genotoxic Drugs, Alkylating agents and Intercalating agents, which are drugs that organize themselves by filling up spaces that are present within the nucleotides in the double helix DNA. They function by interfering with the processes such as transcription, replication and induce mutations. Examples are Doxorubicin, Idarubicin [11] (see Figs. 1 and 2). The identification of topoisomerase in the late twentieth century, led to the explosion of interest in topoisomerase and the advancement of chemicals that can specifically hinder this receptor. Topoisomerase assume an immediate integral part in the usual DNA stands replication. Topoisomerase assist this technique through a reversible trans-esterification reaction, this produces a covalent complex that is formed when the
https://doi.org/10.1016/j.jrid.2019.06.003 2352-6211/© 2019 Beijing You’an Hospital affiliated to Capital Medical University. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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Fig. 1. 3D view of Rubidazone-DNA complex in Topoisomerase II inhibition.
Fig. 2. (a) 3D view of Daunorubicin-DNA complex in Topoisomerase II inhibition, (b) 3D view of VP-16-DNA complex in Topoisomerase II inhibition.
tyrosine part of the compound is bound with the end of 30 phosphotyrosine in a DNA strand. BRCA1 is a fragment of enzyme complex that repairs DNA when both strands are damaged, it interacts with the DNA mismatch repair protein MSH2 [20]. BRCA binds directly to a DNA, but the complexity of branched DNA structures has been reported to significantly increase their interaction. This ability of BRCA to bind to DNA adds to its capacity to constrain the nuclease activity of the MRN complex in addition to the nuclease activity of Mre11 alone [17]. This could be
responsible for the part for BRCA1 in promoting lower conformity DNA repair by Non-Homologous End Joining (NHEJ). Computational methods are useful in making decisions and mimic virtually every aspect of drug discovery and development [14]. For example, in the hit identification phase in which drug discovery teams are provided with many novel chemicals to test for several potential lead molecules that possess the desired drug properties, in silico method of drug discovery would be an ideal method to use [7].
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Table 1 Structure, Name, CAS and NSC number of the complete dataset. Structure
Name
CAS
NSC number
AMONAFIDE
69408-81-7
308847
ANTHRAPYRAZOLE
91440-30-1
355644
BISANTRENE HYDROCHLORIDE
71439684
337766
DAUNORUBICIN
23541-50-6
82151
DEOXEODOXORUBIC-IN
63950-06-1
267469
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Table 1 (continued ) Structure
Name
CAS
NSC number
DOXORUBICIN HYDROCHLORIDE
25316-40-9
357704
m-AMSA (AMSACRINE)
51264-14-3
249992
MENOGARIL
71628-96-1
269148
MITOXANTRON
70476-82-3
301739
VP-16 (ETOPOISOMERASE OSIDE)
33419-42-0
141540
(continued on next page)
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Table 1 (continued ) Structure
Name
CAS
NSC number
RUBIDAZONE
36508-71-1
164011
PYRAZOLOACRIDINE
99009-21-9
366140
OXANTHRAZOLE
105118-12-5
349174
N,N-DIBENZYLDAUNORUBICIN
70878-51-2
268242
Table 2 Molecular docking score of some compound against Human topoisomerase. Title
Entry ID
Score
Nflexi
H-bond
H-phob
VwInt
Eintl
Dsolv
SolEl
AMONAFIDE ANTHRAPYRAZOLE DERIVATIVE BISANTRENE HCl DAUNORUBICIN deoxydoxorubicin DOXORUBICIN m-AMSA MENOGARIL MITOXANTRONE N,N-DIMENZYL DAUNOMYCIN OXANTHRAZOLE PYRAZOLOACRIDINE RUBIDAZONE VP-16
1 2 3 4 5 6 7 8 9 10 11 12 13 14
17.209 19.316 25.022 27.457 24.799 22.58 26.231 17.931 25.843 23.86 21.875 22.225 32.469 23.015
3 9 2 6 7 8 2 5 12 10 10 5 7 5
0.936 5.023 2.24 7.637 4.08 6.685 0 1.41 6.999 3.576 3.675 0 6.438 1.126
3.545 5.068 4.987 5.255 4.719 4.824 5.328 6.259 5.028 7.602 4.988 5.545 6.614 6.131
26.415 29.899 33.589 32.454 35.598 32.331 31.301 29.305 33.272 41.38 34.535 31.234 41.175 36.182
1.781 9.075 3.122 9.511 4.074 15.135 6.801 0 5.1 10.543 7.267 3.138 13.533 5.267
12.268 21.187 16.795 22.108 21.586 26.217 9.327 16.605 20.027 21.617 19.897 10.853 24.41 19.898
4.467 8.177 5.726 11.605 5.898 8.232 0.673 5.579 9.523 14.316 6.634 2.401 10.482 3.332
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Table 3 Molecular docking result of some compound against BRCA1 protein. Title
Entry ID
Score
Nflex
Hbond
Hphob
VwInt
Eintl
Dsolv
SolEl
AMONAFIDE ANTHRAPYRAZOLE DERIVATIVE BISANTRENE HCl DAUNORUBICIN deoxydoxorubicin DOXORUBICIN m-AMSA MENOGARIL MITOXANTRONE N,N-DIMENZYL DAUNOMYCIN OXANTHRAZOLE PYRAZOLOACRIDINE RUBIDAZONE VP-16
1 2 3 4 5 6 7 8 9 10 11 12 13 15
9.174 10.586 12.295 5.527 9.478 9.672 15.821 12.233 1.845 16.859 5.887 3.387 18.619 7.889
3 9 2 6 7 8 2 5 12 10 10 5 7 5
0.445 2.699 1.204 2.818 3.62 5.637 0.915 4.169 3.427 3.312 1.413 0 3.869 2.229
4.895 6.223 6.678 6.258 6.139 6.081 5.441 6.03 5.639 9.194 5.545 5.938 8.862 7.163
10.459 26.374 25.939 27.813 27.925 28.075 24.888 19.412 24.981 40.381 26.245 22.073 40.526 22.084
5.577 3.885 10.775 16.671 10.972 20.433 6.313 0 9.182 25.929 6.534 5.933 27.932 14.684
13.096 11.968 11.725 15.82 18.695 22.5 6.175 16.258 19.899 14.572 19.078 7.993 19.24 14.261
18.814 18.802 16.926 27.489 20.451 22.823 13.934 9.961 20.393 32.02 28.958 30.976 28.794 16.57
Nflex:- Number of Rotatable torsions, Hbond:- Hydrogen Bond energy, Hphob:- Hydrophobic Energy in exposing a surface to water, Vwint:- The Vander Waals Interaction Energy (sum of gc and gh Vander Waals), Eintl:- Internal Conformational Energy of the ligand, Dsolv:- The desolvation of exposed H-bond donors and acceptors, SolEl:- The solvation electrostatics energy change upon binding.
2. Experimental section The equipment and programming utilized in this study and the computational analysis such as for chemical structure optimization, dynamics and docking study incorporates: Computer (HP Intel(R) core i5-4200U with 1.63 Hz and 2.3 Hz processor and windows 8.1), wavefunction Spartan 14.1.4 [10], ChemBio Ultra 12.0 [9,16], Molsoft v3.8.3 software [1,2]. 3. Ligand preparation The 2D structure of each Topoisomerase II inhibitor [3,4] were downloaded as mol files from the chemical book website (http://www.chemicalbook.com/) using their chemical abstract service (CAS) number as presented in Table 1. The structures were introduced into wavefunction 14 graphic user interphase (GUI) after which the 2D structures were converted
into 3D structure by selecting the view dialog box present on Spartan 14 GUI. From the built option on Spartan 14 the structures were cleaned by checking minimize using molecular mechanic force field (MMþ) option in order to remove all strain from the molecular structure. In addition this will ensure a well defined conformer relationship among compounds of the study [19]. From the set up calculation option on Spartan 14, the calculation was set to equilibrium geometry at the ground state using density functional theory at B3LYP (Becke 88 three-parameter hybrid exchange potentials with Lee-YangParr correlation potential) level of theory and 6-311G (d) basis set for the geometrical optimization of the cleansed structures i.e. B3LYP/6-311G (d) level of theory. 4. Preparation of receptor The x-ray diffraction structure of Human topoisomerase II beta with PDB ID: 3QX3 [22] with a resolution 2.16 Å was
Fig. 3. (a) 3D view of VP-16 (8A)-DNA complex in Topoisomerase II inhibition, (b) 3D view of VP-16 (6A)-DNA complex in Topoisomerase inhibition.
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Table 4 VP 16 Derivatives docking results on Human topoisomerase. Entry ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
Term VP-16 8A VP-16 6B VP-16 9A VP-16 8B VP-16 8C VP-16 6A VP-16 9C VP-16 5A VP-16 9B VP-16 7C VP-16 6C VP-16 10A VP-16 4A VP-16 5C VP-16 5B VP-16 7A VP-16 3C VP-16 10B VP-16 10C VP-16 7B VP-16 2A VP-16 1C VP-16 3A VP-16 2C VP-16 2B VP-16 4B VP-16 4C VP-16 3B VP-16 1B VP-16 1A
Score 31.944 31.003 30.775 30.163 30.012 29.797 29.51 28.619 28.388 28.21 27.784 27.482 27.307 26.832 26.768 26.678 26.616 26.323 26.307 25.916 25.34 24.349 24.318 23.986 23.669 23.22 23.044 22.846 20.506 17.04
kI
N-flex
H-bond
H-phob
V-wInt
E-intl
D-solv
SolEl
0.947 0.949 0.949 0.95 0.951 0.951 0.951 0.953 0.953 0.953 0.954 0.955 0.955 0.956 0.956 0.956 0.956 0.957 0.957 0.957 0.958 0.96 0.96 0.96 0.961 0.962 0.962 0.962 0.966 0.972
7 5 8 6 6 7 7 8 7 7 5 6 6 5 5 7 6 6 6 7 6 6 7 5 5 7 7 6 5 5
4.065 4.489 4.049 2.881 2.89 2.962 4.206 2.819 2.895 5.445 2.239 3.347 3.344 2.24 2.259 2.688 2.205 1.805 2.647 2.472 2.888 1.67 1.152 2.648 3.857 1.063 1.12 1.056 1.714 0.797
7.195 6.182 6.704 7.332 7.26 7.409 7.394 6.938 6.88 6.148 6.344 6.027 6.033 6.238 6.247 7.593 6.774 5.989 6.476 6.585 5.58 5.611 6.471 5.41 5.923 6.18 5.677 6.657 6.298 6.277
47.006 38.023 46.782 43.881 43.588 47.958 45.132 45.848 42.978 36.927 38.823 42.997 43.141 39.333 39.343 48.2 38.668 43.033 43.974 40.631 42.821 44.539 43.046 38.779 41.154 38.237 35.619 38.868 37.888 40.121
16.952 10.08 15.253 10.102 8.804 12.707 21.093 16.194 9.401 11.728 8.956 8.749 7.913 8.731 8.264 19.272 10.269 9.118 9.242 12.78 10.284 11.176 8.894 6.97 17.341 6.319 8.544 7.923 9.135 13.95
28.131 21.93 28.451 24.233 24.06 25.628 27.485 23.32 24.624 24.619 20.83 24.872 26.373 21.524 22.076 29.687 21.2 22.532 26.212 23.066 23.613 24.978 23.028 23.439 29.213 20.046 16.696 21.961 23.286 27.501
7.376 4.655 6.977 6.281 6.225 10.908 9.703 10.181 5.84 5.982 3.531 8.739 7.512 4.855 4.423 10.524 4.045 7.257 8.249 5.883 10.934 8.85 6.829 6.874 9.549 3.958 3.774 4.672 8.294 8.602
used for the study. The complexed Etoposide inhibitor was removed from the B-side of 3QX3 where it was covalently bonded with the DNA in the receptor. The receptor structure was imported into the Molsoft.icmpro.v3.8.3 GUI [1,2], and the PDB files was converted into
an ICM-object by removing the additional water molecules confined in the x-ray structure collected from PDB data bank. All the hydrogen atoms were optimized and while some other amino acids such as Histidine, proline, glycine, cysteine etc, which were missing as well as other missing side chains were also treated before the receptor was then applied through the process of molecular docking treatment. 5. Docking method
Fig. 4. 3D view of VP-16 (9A)-DNA complex in Topoisomerase inhibition.
The Human topoisomerase II beta after treatment was docked with the ligands, five types of interaction potentials that represent the receptor pocket including van der Waals potential for a hydrogen atom probe, van der Waals potential for a heavy-atom probe (generic carbon of 1.7A radius), optimizing electrostatic term, hydrophobic terms and loan-pair-based potential, which reflected directional preferences in hydrogen bonding. These energy terms were based on the all-atom vacuum force field ECEPP/3 with added functions to account for solvation free energy and entropic contribution. The conformational sampling in the programme was based on the biased probability Monte Carlo (BPMC) procedure, which randomly selected a conformation in the internal coordinate space and then made a step to a new random position independent of the previous one but according to a predefined continuous probability distribution. It was shown that after each random step, full local minimization
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Table 5 VP 16 Derivatives docking score on BRCA1 protein. Entry ID
Term
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16 VP-16
10C 10B 10A 9C 9B 9A 8C 8B 8A 7C 7B 7A 6C 6B 6A 5C 5B 5A 4C 4B 4A 3C 3B 3A 2C 2B 2A 1C 1B 1A
Score
KI
H-phob
V-wInt
E-intl
D-solv
SolEl
6.128 9.816 5.924 7.628 8.065 13.641 4.055 12.306 7.971 0.170 5.290 11.117 14.131 12.791 15.720 1.161 16.442 11.938 10.893 9.339 7.810 17.354 5.716 2.851 4.767 8.650 7.016 4.351 6.828 1.971
0.990 0.984 0.990 0.987 0.986 0.977 0.993 0.979 0.987 1.000 0.991 0.981 0.976 0.979 0.974 0.998 0.973 0.980 0.982 0.984 0.987 0.971 0.990 0.995 0.992 0.985 0.988 0.993 0.989 0.997
7.756 8.422 8.742 9.287 9.355 8.769 9.230 9.031 10.013 10.389 8.315 8.218 9.393 8.201 8.123 9.682 7.831 7.620 9.936 7.993 8.091 9.527 8.256 9.047 7.859 6.559 6.635 8.803 7.441 7.656
33.122 27.770 31.508 30.746 32.536 29.674 39.101 27.590 34.647 27.020 26.582 29.760 38.969 34.186 34.250 34.772 36.052 33.267 35.199 29.906 24.559 33.956 20.519 25.270 34.848 26.341 24.382 29.367 29.829 21.715
31.013 32.415 26.422 20.032 30.635 21.018 17.048 22.755 23.981 26.772 16.089 28.597 26.207 14.266 15.624 17.822 36.503 23.692 32.611 20.693 12.026 35.092 9.395 33.888 17.595 13.129 11.217 19.167 23.558 12.411
20.670 13.091 18.067 15.247 15.531 14.326 22.094 14.535 17.398 16.369 17.890 16.039 21.924 18.694 18.923 21.762 20.142 18.134 14.519 15.245 13.643 14.986 15.094 14.273 22.141 13.547 19.647 16.372 17.024 15.263
27.778 22.288 27.280 28.063 30.113 17.947 35.439 17.747 28.884 30.338 19.083 23.352 20.147 29.879 28.462 34.920 25.816 28.234 30.401 20.974 16.735 27.648 11.981 29.269 32.175 19.765 18.015 29.370 27.125 19.756
Table 6 Hydrogen and Hydrophobic bond interaction between some ligands and the receptor. Term
Hydrogen Bond (HB) interaction
Bond Length (Å) for HB interaction
Hydrophobic interaction
Rubidazone Daunorubicin m-AMSA Mitoxanthrone Bisantrene HCl VP-16
Dt15, Dc14, Dg13, Da6, Dg7 Dc14, Dt15, Da6, Dg7, Dc8 Dc8 Dc8, Da6 Dg13 Dg13
3.06, 2.74, 2.98 2.65, 3.23, 3.07
Dg5, Da12, Dc8, Dt9 Da12, Dt9, dg13, Dg5 Dt9, Da12, Dg13 Dt9, Da12, Dg13, Dg7, Dc14, Dg5 Da12, Dc8, Dc14 Da12, Dc8, Dt9, Dg10
2.72, 3.25, 2.79, 2.77 3.06, 2.79, 3.85, 3.03 (2.95, 2.73) 2.78
greatly improved the efficiency of the procedure. The ICM program relied on global optimization of the entire flexible ligand in the receptor field and combined large-scale random moves of several types with gradient local minimization and a search history mechanism.
polar solvation energy differences between bound and unbound states, (v) electrostatic energy, (vi) hydrophobic energy, and (vii) hydrogen bond donor or acceptor desolvation. The lower the ICM score, the higher the chance the ligand was a binder.
6. Virtual screening - scoring
7. Designing topoisomerase II inhibitor
The scoring function was used to give a good approximation of the binding free energy between a ligand and a receptor, which was usually a function of different energy terms based on a force-field. The ICM scoring function was weighted according to the following parameters (i) internal force-field energy of the ligand, (ii) entropy loss of the ligand between bound and unbound states, (iii) ligandreceptor hydrogen bond interactions, (iv) polar and non-
The outcome of the ligands docked on Human topoisomerase II beta target was appraised and the interactions of best inhibitors were studied. The bulky side groups and other molecular descriptors presented in the lead compounds were altered to improve on their lethal effect on the cancer cells. This was made successful by incorporating some fragments found to bind intensely with the binding site of the receptor when docked with the same ICM-pro Molsoft program.
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Fig. 5. 3D view of VP-16 (6A)- BRCA1 complex and 2D interaction of VP-16 6A interaction at the binding site.
Table 7 Hydrogen and Hydrophobic bond interaction between the best newly designed ligands and the receptor (Topoisomerase). Term VP-16 VP-16 VP-16 VP-16 VP-16 VP-16
(8A) (6B) (9A) (8B) (8C) (6A)
Hydrogen Bond (HB) interaction
Bond Length (Å) for HB interaction
Hydrophobic interaction
Dg10, Dg10, Dg10, Dg10, Dg10, Dg10,
3.04, 3.15 (2.89, 2.89), (3.18, 3.30) 2.95, 3.16 2.95, 3.10 2.96, 3.10 2.92, 2.94
Dc8, Dt9, Da12, Dc11, Dc8, Dt9, Da12 Dc11, Da12, Dc8, Dt9 Dc11, Da12, Dc8, Dt9 Dc11, Dc8, Dt9, Da12 Dc11, Da12, Dc8, Dt9
Dg13 Dg13 Dg13 Dg13 Dg13 Dg13
8. Validating new drugs for side reaction The newly designed drugs were also studied using molecular docking simulations to investigate their interaction with BRCA1 protein theoretically, the method for this quest was achieved by docking all the compound against the x-ray diffraction Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide PDB ID: 4Y2G [23] with a resolution 2.5 Å gotten from http://www.rcsb.org/. 9. Results and discussion for ligand-receptor docking The ligand-protein docking study done between the receptor topoisomerase and the inhibitors was presented in Table 2. All ligands docking pose were analyzed, they inhibit topoisomerase by intercalating the DNA and thereby inhibiting topoisomerase in the process. In the figures, we realized
that the ligands inhibition mechanisms were found to follow in both hydrophobic and hydrogen bonding interactions with the receptors understudy. Also, the strength of the inhibitors interaction with the receptors were a reflection on the frequency of hydrogen bonds appearing between the ligandprotein complex as shown in Table 2. The result showed a correlation between the score, which was the binding affinity of the compounds reported as free energy of binding in kcal/mol, with the values of the hydrogen bonds, hydrophobic bonds and number of flexible torsions present in the compounds under study. Rubidazone reported with a binding score of 32.469 kcal/ mol was found to have the highest binding affinity; its affinity for the binding site was largely as connected to the value of the hydrogen bond and hydrophobic bond energy, which was reported as 6.438 and 6.614 respectively. The molecular docking study of this ligand, when compared to VP-16 shows the
D.E. Arthur / Radiology of Infectious Diseases 6 (2019) 68e79
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Table 8 Hydrogen and Hydrophobic bond interaction between the best newly designed ligands and the receptor (BRCA1). Term
Hydrogen Bond (HB) interaction
Bond Length (Å) for HB interaction
Hydrophobic interaction
Pi-sigma, Amide interaction
Alkyl/PieAlkyl Interaction
Carbon-Hydrogen Interaction
VP-16 (3C)
Leu 1657, Sep406, Ser 404
(2.68, 2.80), (3.15, 3.09), 2.78
Arg 405
Pro 1659, Val 1654, Phe 1662, Tyr1662, Lys 1702, Leu 1701, Leu 1679
Asn 1678, Sep406
VP-16 (5B)
Leu 1657, Sep406, Ser 404, Asn 1678
2.74, (3.12, 3.17), 3.29, 2.77
e
Val 1654, Leu 1701, Leu 1679
Arg 405, Lys 1702
VP-16 (6A)
Leu 1657, Sep406, Ser 404
(3.08, 2.96), 3.20, 3.11, 2.87
Arg 405
Pro 1659, Phe 1662, Leu 1679, Val 1654
Asn 1678, Lys 1702
VP-16 (6C)
Asn 1678, Ser 404
2.97, 1.89
Phe 1662
Leu 1701, Leu 1679, Ile 1680
Pro 407, Arg 405, Leu 1657, Tyr403
VP-16 (9A)
Ser 404, Sep406
2.06, 2.35
Arg 405
Leu 1679, Leu 1701, Tyr403, Pro 1659
Leu 1657, Lys 1702, Asn 1678
VP-16 (9B)
Sep406, Ser 404
(2.91, 3.16, 3.17), 3.10
Val 1654, Phe 1662, Tyr1666, Arg 405, Gly 1656, Ser 1655, tyr403, Lys 1702, Pro 407, Asn 1678, Leu 1679 Phe 1662, Val 1654, Pro 1659, Leu 1679, Pro 407, Lys 1702, Tyr403, Arg 405 Pro 1659, Phe 1662, Val 1654, Lys 1702, Tyr403, Lys 1702, thr1658, Arg 405, Asn 1678, Lue 1679 Ser 404, Pro 407, Lue 1701, Ile 1680, Leu 1679, Sep 406, Arg 405, Leu 1657, Tyr403, Asn 1678, Pro 1659 Pro 407, Lys 1702, Asn 1678, Leu 1679, Arg 405, Leu 1657, Pro 1659, Phe 1662, Tyr403 Pro 407, Leu 1679, Lys 1702, Arg 405, Tyr403, Leu 1657, Phe 1662, Val 1654, Pro 1659
Arg 405
Phe 1662, Val 1654, Leu 1679, Pro 1659
Leu 1657
Fig. 6. 3D view of VP-16 (9A)- BRCA1 complex and 2D interaction of VP-16 9A interaction at the binding site.
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relevance of some secondary pharmacophore responsible for the interaction involving hydrogen bond-type between the ligands and sugar bases in a human DNA. Other ligands such as DAUNORUBICIN, m-AMSA, BISANTRENE HCl and MITOXANTRONE with binding score for topoisomerase given as 2.7452, 26.231, 25.022 and 25.843 respectively, were reported as the best topoisomerase II inhibitors when ranking their binding score for the most active on Table 2. These ligands were also docked against the enzyme BRCA1 that was a human tumor suppressor enzyme, the binding affinity of the compounds were all less than 20 kcal/ mol, indicating that they were not toxic to the tumor suppressor genes. VP-16 was found to have a low binding score of 7.889 as compared to other ligands that inhibited topoisomerase to a greater extent, such as Rubidazone (18.619), m-AMSA (15.821) and Bisantrene (12.295). The high binding affinity of VP-16 to topoisomerase and low affinity for BRCA1, suggesting that VP-16, though not as active when compared to other ligands, was much less toxic and providing promising opportunities in the designing of new topoisomerase II inhibitor, that was safer to the human body [5,8,15] (see Table 6). The newly designed VP-16 derivatives were docked on topoisomerase and its result reported in Table 7, the result showed that VP-16 (8A) had the highest binding affinity for the receptor, the binding energy (31.944 kcal/mol) placed the ligand as the most active topoisomerase II inhibitor studied here. The number of flexible bonds on the compound was the same as that for the lead compound, suggesting that the improved activity was not a function of the number of flexible torsions but a function of the added secondary pharmacophore responsible for significantly increasing its H-bond at the active site of the receptor. VP-16 (8A) bound to the receptor through hydrogen bond interaction with Dg10 (3.04) and Dg13 (3.15), while the hydrophobic interaction was with Dt8, Da12, Dc8 and Dc11 as seen in Fig. 3. Fig. 3 showed the presence of (pp) areneearene interactions between the ligand and the receptor, this interaction as reported by staker [18], were largely responsible for stabilizing the intercalation of VP-16 (8A) to the DNA-topoisomerase complex (see Fig. 4) (see Table 3). The molecular docking result of the receptoreligand complex for VP-16 (6A), revealed that VP-16 (6A) inserted at the position of DNA cleavage and its binding mechanism was like that of VP-16 (6B). An analysis of VP-16 (6A) complex proved that both ionic forms of the analogues present in the complex was instrumental to their improved binding affinity when compared with VP-16. The binding energy of the VP-16 (6A) to the enzyme topoisomerase was shown in Table 4 was reported as 29.797 kcal/mol. The number of rotatable torsions in the ligand was seven (7) signifying a lot of possible conformational structures within the binding site [6]. The presence of p-p interaction in the analogue with Dc11, Da12, Dc8 and Dt9 confirmed the stable pose of the ligand in the binding pocket. The hydrogen bond present between the hydroxyl group (OH-group) of the ring with Dg10 and Dg13 further contributeed to the high binding score of VP-16 (6A) to the topoisomerase receptor.
VP-16 (9A) inhibited Topoisomerase with a binding energy of 30.775 kcal/mol, the bulk of this energy contribution was from the Vander Waals interaction and hydrophobic energy (43.881 and 6.704 and respectively), while the hydrogen energy (H-bond energy) was given as 4.094. VP-16 (9A) intercalateed with DNA to inhibit the topoisomerase enzyme, by forming many areneearene (p-p) interaction with Dc11, Da12, Dc8 and Dt9, this p-p interaction stabilizes the VP-16 analogue [21]. While the presence of alkoxy-group on VP16(9A) increaseed its binding affinity by forming hydrogen bonds with surrounding Dg10 and Dg13 and the corresponding bond lengths (2.95)Å and 3.16 Å respectively as shown in Fig. 3(b), confirming the relationship between the binding affinity and the alkoxy group present in analogue VP-16(9A). All analogues of VP-16 drug bound to the protein BRCA1 satisfactorily, though their reported binding affinity presented in Table 5, which was reported to be low with values ranging from 0.170 to 17.351. It showed that the newly designed derivatives of VP-16 could be used as preferred substitute for the other topoisomerase II inhibitors studied in this work. The interactions of VP-16(A) captured in Fig. 5, indicated the presence of an amide pi stacked interaction with Arg 405, hydrogen bond interaction with Leu 1657, Sep406, Ser 404 with the corresponding bond lengths of (3.08, 2.96), 3.20, 3.11, 2.87, piealkyl interaction with Pro 1659, Phe 1662, Leu 1679, Val 1654 and finally a carbon-hydrogen bond type with Asn 1678, Lys 1702 were responsible for its stability. Other noticeable analogue such as VP-16(9A) interactions with BRCA1 were also presented in Table 8, its 2D interaction was shown in Fig 6. More than 10 interaction contacts were noticed within the complex binding site and this could be attributed to the large flexible bonds in VP-16(9A). These results were promising and superior to other Topoisomerase II inhibitors docking results carried out within this study, and hence making VP-16(8A, 8B and 6A) the most active and less toxic topoisomerase II inhibitor . 10. Conclusion The docking study done amid at the target Topoisomerase (PDB: 3QX3) and the studied inhibitors were found to be successfully completed using a molsoft program. The inhibitors were found to prevent the enzyme from completing their primary function by wholly lodging the active sites in the intended receptor; the mechanism for this reaction was the same in all cases, which took into account of the ligands intercalated through covalently joined Topoisomerase-DNA complex. The compounds with the highest binding affinity for the enzyme was employed, to design new analogues, thus successfully enhancing the bioactivity of the lead compound. VP-16 analogues designed considerably different in bioactivity from the lead compound since by addition of heterocontaining groups, as well as other highly electronegative elements such as the halide groups, were responsible for enhancing the binding energy of the ligand. This was evident when the number of hydrogen bonds interaction present in the complex were increased. In conclusion, our research proposed
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a better anticancer drug, which was computationally validated and were found to be more potent, less toxic when used as topoisomerase oisomerase II inhibitors. VP-16 (8A) through the binding energy of 39.144 kcal/mol was confirmed to be the best inhibitor, since its binding energy, when entangled with topoisomerase oisomerase, far surpassed other ligands that were studied. Therefore, we hope that future studies, would take into account of the synthesis and experimental validation of this novel analogues clearly accessible in this manuscript in order to affirm our theory. References [1] Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235(3):983e1002. [2] An J, Totrov M, Abagyan R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol Cell Proteom 2005; 4(6):752e61. [3] Arthur DE, Uzairu A, Mamza P, Abechi E, Shallangwa G. Qsar modelling of some anticancer PGI50 activity on hl-60 cell lines. Albanian J Pharm Sci 2016;3(1):4e9. [4] Arthur DE, Uzairu A, Mamza P, Abechi S. Quantitative structureeactivity relationship study on potent anticancer compounds against MOLT-4 and P388 leukemia cell lines. J Adv Res 2016;7(5):823e37. [5] Chen L, Chen X. Results of molecular docking as descriptors to predict human serum albumin binding affinity. J Mol Graph Model 2012;33:35e43. [6] Cremer Dt, Pople J. General definition of ring puckering coordinates. J Am Chem Soc 1975;97(6):1354e8. [7] Damme SV, Bultinck P. A new computer program for QSAR-analysis: ARTE-QSAR. J Comput Chem 2007;28(11):1924e8. [8] Davis GDJ, Vasanthi AHR. QSAR based docking studies of marine algal anticancer compounds as inhibitors of protein kinase B (PKBb). Eur J Pharm Sci 2015;76:110e8. [9] Evans DA. History of the harvard ChemDraw project. Angew Chem Int Ed 2014;53(42):11140e5. [10] Hehre WJ, Huang WW. Chemistry with computation: an introduction to SPARTAN. Wavefunction, Inc; 1995. [11] Herrlich P, Morrison H, Sleeman J, ORIAN-ROUSSEAU V, K€onig H, WEG-REMERS S, et al. CD44 acts both as a growth-and invasivenesspromoting molecule and as a tumor-suppressing cofactor. Ann N Y Acad Sci 2000;910(1):106e20.
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