Modeling studies on the Interactions of Endocrine Disruptive Compound BPA and its Analogs with dsDNA

doi:10.21203/rs.3.rs-4890808/v1

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Modeling studies on the Interactions of Endocrine Disruptive Compound BPA and its Analogs with dsDNA

https://doi.org/10.21203/rs.3.rs-4890808/v1

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BPA and its derivatives have been used heavily in the manufacture of epoxy resins and polycarbonate plastics. They are mainly used in food packaging materials, dental sealants and thermal receipts. Human beings are subjected to the exposure of BPA through their diet via consumption of packed food materials. Previous studies have revealed diverse disadvantages of BPA and its halogen derivatives on plants growth and also on human body. Present work is dedicated to the detailed study of interaction between DNA and BPA derivatives through computational tools. Five different BPA derivatives namely BPA, BPAF, BPS, TBBPA and TCBPA were selected as ligands for the study whereas 5 DNA sequences with PDB ID 1BNA, 1DSC, 1RMX, 2ROU and 195D were taken as macromolecular targets. Firstly, geometry optimization of the ligands was performed and then they were subjected to three computational analysis methods, Molecular Docking, Molecular Dynamics and Quantum Mechanical/Molecular Mechanical (QM/MM) respectively. Such investigations would aid in better understanding of the toxic mechanism of BPA and bring about new scientiﬁc insights about other Bisphenol A analogues.

Computational Biology

BPA

BPAF

BPS

Molecular Docking

Molecular Dynamics.

Bisphenol A is a compound which falls in the class of chemicals generally called as diphenylmethanes. Compounds of this class contain two benzene rings separated by one central carbon atom, usually with a para-hydroxy group on both benzene rings [1]. It is an estrogenic EDC i.e., endocrine disrupting compound. BPA is called estrogenic EDC as it mimics estrogen [2]. Being a xenoestrogen, it disrupts the hormonal balance in the human body [3]. BPA and its derivatives have been used heavily in the manufacture of epoxy resins and polycarbonate plastics. They are mainly used in food packaging materials, dental sealants and thermal receipts. Human beings are subjected to the exposure of BPA through their diet via consumption of packed food materials [4]. BPA which is used in food packaging materials can leak into the food or get mixed with it. Because of long preservation time period, storage condition like temperature pressure or packing technique the chemical constituents of packing material may get migrate into the food which may cause severe health issues [5]. Previous studies have revealed diverse disadvantages of BPA and its halogen derivatives on plants growth and also on human body. Due to their tendency to affect photosynthesis, they are a risk for the development and growth of plants and because of endocrine disrupting activities they are a threat to human body also [6-8]. A number of studies since a long time indicate the miserable effects due to BPA exposure in adults [9]. It may lead to various health associated problems like reduced ovarian response and IVF success, decrease in fertilization success rate and embryo quality, miscarriage, abnormal and premature delivery, reduced male sexual function, reduction in sperm quality, PCOS, alteration in the concentration of thyroid hormone, type-2 diabetes, cardiovascular disease (i.e. heart disease, hypertension, and cholesterol levels), altered liver function, obesity, albuminuria, oxidative stress and many more. BPA has also been supposed to affect breast cancer and prostate cancer development [10-12]. The severe effect of BPA on the development of children and various health issues lead to the restriction of use of BPA in the manufacture of baby food containers and other food containers [13, 14]. After this several derivatives of BPA came in highlight which can act as an alternative of BPA. As a consequence, existence of bisphenol S (BPS), bisphenol F (BPF) and bisphenol AF (BPAF) in many daily use food and products including vegetables, meat, seafood and dairy products is very common now-a-days. But are these derivatives safe enough is a question of concern. If bromine or chlorine is substituted at the phenolic ring of BPA, we get halogenated derivatives of BPA. These are mainly used in the form of flame retardants (FRs) to decrease the flammability of polymers. The name of bromine substituted derivatives is TBBPA (Tetrabromobisphenol A) whereas chlorine substituted derivative is called TCBPA (Tetrachlorobisphenol A). TBBPA and TCBPA are generally used as FRs in the polymer industry. These derivatives are also dangerous for the environment as their continous use enhance contamination in the environment [15]. Understanding and analysis of the mechanism by which BPA and its derivatives effects different functions of human body is a matter of great concern and it requires a lot of research work. A number of studies have been done on the effect of BPA on humans in last few years but unfortunately the studies on its derivatives are not enough [16-18].The alternatives of BPA which are currently used in the industries are just derivatives of BPA which can be as hazardous as BPA [19-22]. It is need of the hour to investigate the functionality, mechanism and effects of such compounds like BPS, BPAF, TBBPA, TCBPA etc on human health. The genotoxic and endocrine activities of BPF and its metabolites were examined by Cabaton et al. (2009) and it was found that the most toxic compound was BPF compare d to its other metabolites identiﬁed in rat urine [23]. Another study tells that alike BPA and BPS, other bisphenols derivatives BPF and BPAF have been found in the urine of humans [24]. BPS (bisphenol S) also acts as an EDC (endocrine disruptor compound) similar to BPA [25]. As BPS is more stable in response to heat and light effects than BPA, its degradation in sea water is very hard and remains a persistent toxic pollutant compared with BPA [26]. These properties of BPS indicate a high pollution potential for BPS as it is used more and more [27]. However, no biotransformation studies have been performed for other BPA analogs such as bisphenol AF (BPAF), bisphenol Z (BPZ), TBBPA (Tetrabromobisphenol A), TCBPA (Tetrachlorobisphenol A) etc. Some of the previous studies indicate the interaction of BPA and its analogs with DNA [28]. An oxidation product of 3-hydroxy-BPA is ortho-quinone BPA, which has been reported to form adducts with DNA in vitro and in vivo [29]. The reaction of bisphenol A 3,4-quinone with DNA is studied by Edmonds et.al,[30]. Wang et. al. in 2014 studied the interaction of BPS with DNA and concluded the minor groove binder nature of BPS [31]. In order to comprehend the toxic effects or chemotherapeutic effects of small compounds, much attention has recently been paid to their binding interactions with DNA [32–34]. Bisphenol A and its analogues' molecular interactions with serum albumin have been researched up to this point. As an illustration, Xie et al investigation of the interaction between BPA and human serum albumin revealed the presence of hydrophobic forces in the BPA–HSA interaction [35]. DNA is the macromolecular target of many drugs. Interaction with DNA is a significant part of the study of a compound for being a useful drug against certain disease [36,37]. There are only few a works which are dedicated to the interaction of BPA and BPA derivatives with DNA [38,39]. Present work is dedicated to the detailed study of interaction between DNA and BPA derivatives through computational tools. Five different BPA derivatives namely BPA, BPAF, BPS, TBBPA and TCBPA were selected as ligands for the study whereas 5 DNA sequences with PDB ID 1BNA, 1DSC, 1RMX, 2ROU and 195D were taken as macromolecular targets. Molecular Docking studies of different azole derivatives with DNA segment with PDB ID 2ROU. Firstly, geometry optimization of the ligands was performed and then they were subjected to three computational analysis methods, Molecular Docking, and Molecular Dynamics Simulations. Molecular Docking informs about the possible interaction of selected 5 BPA compounds with DNA. The result from docking process provides the input for molecular dynamics simulation which investigate the time dependent characteristics of the system. Such investigations would aid in better understanding of the toxic mechanism of BPA and bring about new scientiﬁc insights about other Bisphenol A analogues.

Computational Details

Dataset: The pdb format file of DNA sequences with PDB ID - 1BNA, 1DSC, 1RMX, 2ROU and 195D were sourced from RCSB ‘Protein Data Bank’ (PDB)[41]. All crystallographic water and small molecules were removed from the DNA sequences by the help of UCSF Chimera Software[42]. Hydrogen atoms were also added. Table 1 shows the PDB ID and sequence of the DNA segment used. The structures of BPA, BPAF, BPS, TBBPA and TCBPA were collected from literature [43, 44]. Figure 1 shows the chemical structures of these drugs. These structures were designed using Gaussview5.0 software [45].

Molecular Docking

Molecuar Docking process between the ligands and DNA segments was performed using AUTODOCK4 software [47]. Autodock tools with Lamarckian Genetic Algorithm (LGA) was implemented. Firstly, macromolecule was prepared in the form of PDBQT file [48]. Then, ligand was also prepared and saved as a PDBQT file. After preparation of macromolecule and ligand, grid boxes of various dimensions were prepared for each complex system and grid calculations were performed. Second step is the docking calculations. Docking was performed and dlg type file is the output file which gives the details of the docking process. For each drug-DNA docking, several poses of drug with DNA are docked. For each pose, binding energy is calculated and each pose is given an Autodock generated score function. The pose with lowest value of binding energy is considered as final binding mode.

Table 1. PDB ID and sequence of the DNA used.

S. No.	DNA Sequence	PDB Id
1	5'-CGCGAATTCGCG-3'	1BNA
2	5'-GAAGCTTC-3'	1DSC
3	5'-CGACTAGTCG-3'	1RMX
4	5'-ATCGCGCGGCATG-3'	2ROU
5	5'-CGCGTTAACGCG-3'	195D

Molecular Dynamics

Molecular dynamics simulations provide a great deal of information on nucleic acids and proteins' fluctuations, stability, and conformational changes. These methods are now routinely used to investigate the dynamics, structure, and thermodynamics of biomolecules and their complexes [49]. In the present work, MD simulations were carried out using GROMACS 5.0.4 software [50]. The best-docked poses of DNA-ligand complexes from the docking studies have been submitted to molecular dynamics simulations for the time-dependent study of the formation of the complexes and their stability. After the analysis of molecular docking process, two complex systems namely BPS and TBBPA with DNA segment 1BNA were subjected to molecular dynamics simulations of 100ns each. The AMBER force fields [51] appear to be good for nucleic acid simulation due to the presence of unusual topologies for the terminal nucleotides, despite the fact that there are numerous studies on force fields accessible for molecular dynamics simulations of nucleic acids. For the purpose of creating a topology file for the chosen DNA sequence, the GROMACS software suite's Amber03 force field was used. To generate an octahedral box for the ligand-DNA solvation at 298K, the software's TIP3P water model was used [52]. The system was then neutralised by adding sodium ions to the solvated box holding the DNA-ligand complex by randomly replacing the water molecules. Long-range electrostatic interactions were handled using Particle Mesh Ewald (PME) [53]. Using the Steepest Descent leap-Frog Integration Method, the entire system's energy minimization was done in 25000 steps. This was followed by NVT ensemble equilibration at a constant temperature of 300K for 50s using a Berendsen thermostat [54]. The system was then equilibrated using a steepest descent leap-frog integrator with an NPT ensemble at a constant pressure of 1 atm over a period of 25000 steps. [55]. XMgrace software was used to plot the graphs [56].

Geometry Optimization

Figure 3 represents the three-dimensional optimized geometries of all the ligands after optimization by Gaussian 09 software at B3LYP density functional with basis set 6-31G. These optimized ligands were used as initial inputs for the molecular docking process [57].

Molecular Docking

In an attempt to find the mode of binding of various drugs with DNA structures, molecular docking tool was used in the present study. It is an important and effective tool to gain information regarding the structural characteristics of ligand-macromolecule complexes and the binding efficiency of a ligand with its receptor, which can support and verify the experimental results. The results obtained from molecular docking done by Autodock software for each DNA sequence are summarized in below sections. Molecular docking studies were done for the five sets of DNA segments in search of their preferential binding modes, corresponding binding affinities and for gaining atomistic insights regarding the factors that contribute to the stable complex formation.

BPA & its Analogs with 1BNA

Binding energies obtained from computational docking method for the DNA sequence with PDB ID 1BNA is tabulated in Table 2. From the resulting docking complexes, as given in Table 3 and shown in Fig. 3., it is quite clear that the manner of binding interaction of BPA derivatives with sequence 1BNA shows mainly minor groove binding. The main reason for this type of binding was mainly the structure of the DNA sequence. TBBPA-DNA complex has largest binding energy which means this complex is most tightly bonded and it is most stable.

BPA & its Analogs with 1DSC

Binding energies obtained from computational docking method for the DNA sequence with PDB ID 1DSC is tabulated in Table 2. From the resulting docking complexes, as given in Table 3 and shown in Fig. 4, it is quite clear that the mode of binding interaction of BPA derivatives with sequence 1DSC shows mainly minor groove binding. TBBPA-DNA complex has largest binding energy which means this complex is most tightly bonded and it is most stable. The mode of binding of TBBPA with DNA is different from others. It is bound in the minor groove as well as in the intercalation gap of the DNA sequence.

BPA & its Analogs with 1RMX

Binding energies obtained from computational docking method for the DNA sequence with PDB ID 1RMX is tabulated in Table 2. From the resulting docking complexes, as given in Table 3 and shown in Fig. 5., it is quite clear that the manner of binding interaction of BPA derivatives with sequence 1RMX shows mainly minor groove binding. TBBPA-DNA complex has largest binding energy which means this complex is most tightly bonded and it is most stable. The mode of binding of TBBPA with 1RMX is major groove binding which is different from others. It is bound in the major groove of the DNA segment.

BPA & its Analogs with 2ROU

Binding energies obtained from computational docking method for the DNA sequence with PDB ID 2ROU is tabulated in Table 2. From the resulting docking complexes, as given in Table 3 and shown in Fig. 6., it is simply clear that the mode of binding interaction of BPA derivatives with sequence 1RMX shows both minor groove binding and intercalation. TBBPA and TCBPA forms intercalative complex with 2ROU. The availability of intercalation gap makes the larger size compounds to attach there. Here also TBBPA has largest binding energy which means this complex is most tightly bonded and it is most stable.

BPA & its Analogs with 195D

Binding energies obtained from computational docking method for the DNA sequence with PDB ID 195D is tabulated in Table 2. From the resulting docking complexes, as given in Table 3 and shown in Fig. 6., it is simply clear that the mode of binding interaction of BPA derivatives with sequence 195D shows both minor groove binding and intercalation. TBBPA and TCBPA forms intercalative complex with 195D. The availability of intercalation gap makes the larger size compounds to attach there. Here also TBBPA has largest binding energy which means this complex is most tightly bonded.

Table 2

Binding energies (kcal/Mol) of ligands with different DNA sequences.
Ligands	1BNA	1DSC	1RMX	2ROU	195D
BPA	-5.34	-5.10	-6.02	-5.33	-5.45
BPAF	-5.48	-4.52	-5.49	-5.35	-4.95
BPS	-5.25	-4.68	-5.87	-5.91	-5.68
TBBPA	-7.53	-6.91	-6.16	-7.16	-8.12
TCBPA	-7.06	-6.42	-5.72	-6.24	-7.18

Table 3

Binding mode of ligand-DNA complex system. (MI-minor groove binding, MA-major groove binding, IN-intercalation).
Ligands	1BNA	1DSC	1RMX	2ROU	195D
BPA	MI	MI	MI	MI	MI
BPAF	MI	MI	MI	MI	MI
BPS	MI	MI	MI	MI	MI
TBBPA	MI	IN & MI	MA	IN	MI
TCBPA	MI	MI	MI	IN	MI

Hydrogen Bond Interaction Analysis

For each drug-DNA complex system's optimal docked pose, detailed hydrogen bond analysis was performed to get total information about the importance of hydrogen binding in the stability of the considered complex system. Three-dimensional system configuration was obtained to identify the residues of the DNA and atoms of the ligands connected in the hydrogen bonding. This was done with the help of Discovery studio visualizer [5]. Figure 8–12 shows the donor and acceptor region between the ligand and DNA residues for the best docked pose of each DNA-ligand system. In order to establish stability [42] during the docking computations, the clouded patches in the figure depict the atoms or groups of atoms that have a capacity to give or take electrons for hydrogen bonding.

Table 4

The donor species, acceptor species and H-bond length formed between the ligands and 1BNA
S.No.	DNA	Ligand	No. of H-bonds	Interacting species	H-bond length(Å)
1.	1BNA	BPA	2	UNK0:H - B:DT20:O2 A:DG4:N2 - :UNK0	2.146658 3.425313
		BPAF	5	A:DA6:C5' - :UNK0:F UNK0:H - B:DC23:O4' B:DG22:C5' - :UNK0:F B:DG22:C5' - :UNK0:F UNK0:H - B:DT20:O2	2.953399 1.974467 3.322622 2.920749 2.107035
		BPS	2	A:DA6:C5' - :UNK0:O B:DG22:N2 - :UNK0:O	3.107792 3.027773
		TBBPA	4	UNK0:H - A:DC9:O3' B:DT19:C5' - :UNK0:O B:DA17:C2 - :UNK0:Br B:DA17:C2 - :UNK0:Br	2.653264 3.460350 3.688278 3.688278
		TCBPA	4	UNK0:H - A:DC9:O3' B:DT19:C5' - :UNK0:O B:DA17:C2 - :UNK0:Cl B:DA17:C2 - :UNK0:Cl	2.496548 3.467059 3.422616 3.422616
2.	1DSC	BPA	3	B:DA11:H1' - :UNK0:O UNK0:H - B:DG12:O4' UNK0:H - A:DC5:O4'	2.592223 1.948967 1.985355
		BPAF	6	UNK0:H - A:DC5:O4' A:DT6:H4' - :UNK0:F A:DT6:H4' - :UNK0:F A:DT6:H1' - :UNK0:F A:DT7:H5'1 - :UNK0:F UNK0:H - B:DG12:OP	1.846534 2.478208 2.400654 2.124977 2.018987 1.616678
		BPS	4	B:DG12:H21 - :UNK0:O UNK0:H - A:DC5:O4' UNK0:H - A:DG4:OP1 B:DT15:H1' - :UNK0:O	3.082238 1.795986 2.093244 2.868413
		TBBPA	1	A:DG4:H1' - :UNK0:Br	2.858970
		TCBPA	3	UNK0:H - A:DC5:OP1 UNK0:H - B:DT15:O3' B:DC16:H5'1 -UNK0:Cl	1.920369 1.848536 2.829143
3.	1RMX	BPA	4	B:DG17:H22 - UNK0:O UNK0:H - B:DT18:O2 UNK0:H - A:DG2:N3 UNK0:H - A:DA3:O4'	2.205445 1.954476 2.844300 2.000574
		BPAF	8	UNK0:H - B:DC14:O4' UNK0:H - B:DA16:O4' A:DT8:H1' - :UNK0:F A:DT8:H4' - :UNK0:F A:DG7:H22 - :UNK0 B:DT15:H5'1 - UNK0:F B:DT15:H4' - :UNK0:F A:DG7:H22 - :UNK0	1.849773 1.942170 2.607677 2.646219 2.326485 2.638398 2.456756 2.326485
		BPS	3	A:DG7:H4' - :UNK0:O A:DA6:H1' - :UNK0:O B:DG17:H22 - :UNK0:O	2.739161 2.368616 2.511983
		TBBPA	4	UNK0:H - A:DG2:OP2 UNK0:H - B:DG17:O6 A:DC4:H42 - :UNK0:O A:DA3:H8 - :UNK0:Br	1.649261 1.933400 2.766324 2.457550
		TCBPA	2	UNK0:H - A:DG7:O3' A:DT5:H4' - :UNK0:Cl	1.920755 2.829540
4.	2ROU	BPA	4	UNK0:H - B:DC23:O4' UNK0:H - B:DG24:N3 UNK0:H - B:DA25:O4' B:DA25:H5'1 - UNK0:O	2.112552 2.593854 2.288214 2.083864
		BPAF	7	UNK0:H - B:DC23:O4' A:DC5:H1' - :UNK0:F A:DC5:H4' - :UNK0:F A:DG4:H21 - :UNK0 B:DG24:H4' - :UNK0:F B:DG24:H22 - :UNK0:O UNK0:H - B:DA25:O4'	1.971740 2.301018 2.471182 2.795444 2.566168 1.897726 2.059780
		BPS	4	B:DG22:H22 - :UNK0:O UNK0:H - B:DC23:O4' B:DG24:H22 - :UNK0:O UNK0:H - B:DA25:O4'	1.811454 2.086173 1.759489 1.931819
		TBBPA	2	UNK0:H - B:DG22:O3' B:DG22:N3 - :UNK0:Br	1.907082 3.364273
		TCBPA	1	UNK0:H - B:DG22:O3'	1.956736
5.	195D	BPA	6	UNK0:H - A:DG10:O4' UNK0:H - A:DC9:O2 B:DG16:N2 - :UNK0 A:DG10:N2 - :UNK0 B:DG14:N2 - :UNK0:O UNK0:H - B:DC15:O2	2.024700 3.010265 3.366872 3.732183 2.963752 2.255529
		BPAF	6	UNK0:H - A:DA7:O4' UNK0:H - A:DT6:O2 A:DT6:C4' - :UNK0:F B:DC21:C4' - :UNK0:F B:DG22:C5' - :UNK0:F B:DG22:C5' - :UNK0:F	2.914469 2.242876 3.275043 3.445188 3.440485 3.112585
		BPS	6	B:DT18:C5' - :UNK0:O UNK0:H - A:DC11:O2 A:DG10:N2 - :UNK0 B:DG16:N2 - :UNK0 B:DG16:N2 - :UNK0 UNK0:H - A:DC9:O4'	3.131961 1.868998 3.904925 3.360563 4.150626 2.103495
		TBBPA	3	UNK0:H - A:DG10:OP1 B:DA19:C5' - :UNK0:Br UNK0:H - B:DT18:O2	1.671796 3.493976 2.026440
		TCBPA	3	UNK0:H - A:DG10:OP1 UNK0:H - B:DT18:O2 A:DA7:C2 - :UNK0:O	1.779204 1.929722 2.838304

Hydrophobic Interaction Analysis

Hydrophobic binding is the main type of binding involved in the case of intercalation between ligand and DNA. As TBBPA interacts with 1DSC and 2ROU as an intercalator, hydrophobic bonding dominates there. In the case of intercalative binding, small drugs get stacked in between the bases of DNA. In this stacking, hydrophobic bonds are responsible for the binding between the ligand and DNA. Table 5 gives the hydrophobic bond details for DNA-ligand complex systems. Number of hydrophobic bonds, involved species and bond length for each bond for all of the complexes is given. It is clear from the table that this binding is dominating over hydrogen binding in the case of intercalation. TBBPA-1DSC has maximum number of hydrophobic bonds (15) between them.

Table 5

Hydrophobic bond details for DNA-ligand complex systems.
S.No.	DNA	Ligand	No. of H-bonds	Interacting species	H-bond length(Å)
1.	1BNA	BPA	1	A:DA6 - :UNK0	5.640001
		BPAF	-	-	-
		BPS	-	-	-
		TBBPA	8	A:DG10 - :UNK0:C B:DA17 - :UNK0:C B:DA17 - :UNK0:C B:DG16 - :UNK0:C A:DC9 - :UNK0:Br B:DA17 - :UNK0:Br B:DA18 - :UNK0:Br B:DA18 - :UNK0:Br	5.107532 4.789819 4.629728 5.231530 5.100588 4.855225 4.953848 4.583980
		TCBPA	5	A:DG10 - :UNK0:C B:DG16 - :UNK0:C B:DA18 - :UNK0:Cl A:DC9 - :UNK0:Cl B:DA18 - :UNK0:Cl	5.057249 5.290743 4.919593 4.826548 4.515906
2.	1DSC	BPA	-	-	-
		BPAF	-	-	-
		BPS	2	A:DG4:H1' - :UNK0 A:DG4 - :UNK0	2.688382 5.428517
		TBBPA	15	A:DG4 - :UNK0 A:DG4 - :UNK0 B:DG12 - :UNK0 B:DG12 - :UNK0 A:DC5 - :UNK0 B:DG12 - :UNK0:Br B:DG12 - :UNK0:Br A:DG4 - :UNK0:Br A:DG4 - :UNK0:Br A:DG4 - :UNK0 A:DG4 - :UNK0 A:DA3 - :UNK0 A:DA3 - :UNK0:Br A:DA2 - :UNK0:Br A:DG4 - :UNK0:C	3.660076 3.472163 5.044223 4.137928 5.078582 4.615677 4.092550 4.413255 5.348134 4.214586 5.243034 5.851540 4.566702 4.848568 4.685772
		TCBPA	6	A:DG4 - :UNK0:C UNK0:C - A:DG4 A:DG4 - :UNK0:C A:DA3 - :UNK0:C A:DA3 - :UNK0:C B:DT15 - :UNK0	4.577710 3.956262 4.170467 4.723995 3.924687 5.804858
3.	1RMX	BPA	2	B:DG20 - :UNK0 A:DA3 - :UNK0	5.322433 5.746136
		BPAF	4	B:DA16 - :UNK0 B:DA16 - :UNK0 B:DC14 - :UNK0 A:DG7 - :UNK0	5.847956 5.701454 5.233760 5.442357
		BPS	4	B:DG17 - :UNK0 B:DA16 - :UNK0 B:DA16 - :UNK0 B:DA16 - :UNK0	5.245217 5.593453 4.614065 5.226543
		TBBPA	10	A:DC1 - :UNK0:C A:DG2 - :UNK0:C A:DG2 - :UNK0:Br A:DA3 - :UNK0:Br A:DA3 - :UNK0:Br B:DT18 - :UNK0:Br B:DG17 - :UNK0:Br B:DG17 - :UNK0:Br B:DA16 - :UNK0:Br B:DA16 - :UNK0:Br	4.059302 4.762154 4.163649 4.444690 5.062381 5.369911 5.394669 4.700506 5.406580 4.253863
		TCBPA	1	A:DG7 - :UNK0:Cl	4.936818
4.	2ROU	BPA	4	UNK0:H- :DC23:O4' UNK0:H- B:DG24:N3 UNK0:H- :DA25:O4' B:DA25:H5'1- NK0:O	2.112552 2.593854 2.288214 2.083864
		BPAF	7	UNK0:H- B:DC23:O4' A:DC5:H1' - :UNK0:F A:DC5:H4' - :UNK0:F A:DG4:H21 - :UNK0 B:DG24:H4'- UNK0:F B:DG24:H22-NK0:O UNK0:H- :DA25:O4'	1.971740 2.301018 2.471182 2.795444 2.566168 1.897726 2.059780
		BPS	4	B:DG22:H2-UNK0:O UNK0:H- :DC23:O4' B:DG24:H2-UNK0:O UNK0:H- :DA25:O4'	1.811454 2.086173 1.759489 1.931819
		TBBPA	2	UNK0:H- :DG22:O3' B:DG22:N3-UNK0:Br	1.907082 3.364273
		TCBPA	1	UNK0:H- :DG22:O3'	1.956736
5.	195D	BPA	6	UNK0:H- :DG10:O4' UNK0:H - A:DC9:O2 B:DG16:N2 - :UNK0 A:DG10:N2 - :UNK0 B:DG14:N2- UNK0:O UNK0:H- B:DC15:O2	2.024700 3.010265 3.366872 3.732183 2.963752 2.255529
		BPAF	6	UNK0:H - A:DA7:O4' UNK0:H - A:DT6:O2 A:DT6:C4' - :UNK0:F B:DC21:C4'- UNK0:F B:DG22:C5'- UNK0:F B:DG22:C5'- UNK0:F	2.914469 2.242876 3.275043 3.445188 3.440485 3.112585
		BPS	6	B:DT18:C5'- UNK0:O UNK0:H- A:DC11:O2 A:DG10:N2 - :UNK0 B:DG16:N2 - :UNK0 B:DG16:N2 - :UNK0 UNK0:H - A:DC9:O4'	3.131961 1.868998 3.904925 3.360563 4.150626 2.103495
		TBBPA	3	UNK0:H - A:DG10:OP1 B:DA19:C5' - :UNK0:Br UNK0:H - B:DT18:O2	1.671796 3.493976 2.026440
		TCBPA	3	UNK0:H - A:DG10:OP1 UNK0:H - B:DT18:O2 A:DA7:C2 - :UNK0:O	1.779204 1.929722 2.838304

Molecular Dynamics

TBBPA has maximum binding energy amongst all of the compounds whereas BPS has lowest for 1BNA complexes. So, molecular dynamics simulations were performed for both TBBPA-1BNA complex and BPS-1BNA complex. The time for each simulation was taken to be 100 ns. As 1BNA is a B-type DNA which is prominent in human body so the simulations are carried out using complexes of 1BNA and ligands. The most preferred binding mode obtained from molecular docking calculations was taken as initial structures for MD simulations for the stability study of DNA-ligand complexes. All simulations were carried out using Gromacs, as discussed in the method section. For both systems variation of hydrogen bonds, RMSD curves, RMSF curves and radius of gyration variation curves were plotted. The details are discussed below.

MD results for TBBPA-1BNA complex

The results from MD simulations were analysed in the form of trajectories. Figure 13 gives the trajectories for 1BNA-TBBPA complex. Figure 13(a) represents the average number of hydrogen bonds formed for the system during the simulation process. As clear from the figure, TBBPA form an average of 2 hydrogen bonds with DNA during the simulation process. Figure 13(b) represents the RMSD (root mean square deviation) curve for both DNA and the ligand. The RMSD serves as a measure for biological macromolecules' structural stability. It is clear from the figure that the deviation for both DNA and ligand lie well in the range 1Å − 4Å, showing stability of the complex for the 100 ns of simulation. Figure 13(c) represents the RMSF (root mean square fluctuation) curve for the system. RMSF keeps track of changes in each amino acid base pair over the course of the MD simulation, as well as changes in the nucleic acid's flexible areas. High- and low root mean square fluctuations levels, respectively, distinguish loosely bound and tightly bound sections in the DNA strands. The figure gives the RMSF curve which represent insignificant fluctuations. Figure 13(d) represents the variations in the radius of gyration for the complex system. To understand the compactness of DNA and the dynamical stability of DNA-ligand complex systems, values of radii of gyration were obtained. These variations in energies were obtained through gmx_gyrate programme inbuilt in GROMACS software suite.

MD results for 1BNA-BPS complex

The results from MD simulations were analysed in the form of trajectories. Figure 14 gives the trajectories for 1BNA-BPS complex. Figure 14(a) represents the average number of hydrogen bonds formed for the system during the simulation process. As clear from the figure, BPS form maximum number of 3 hydrogen bonds with DNA during the simulation process. Figure 14(b) represents the RMSD (root mean square deviation) curve for both DNA and the ligand. The RMSD serves as a measure for biological macromolecules' structural stability. It is clear from the figure that the deviation for ligand lie well in the range 1Å − 4Å, but the case for DNA is not similar. After 40ns, the curve for DNA shows deviations inconsistent with previous data. For 40ns-100ns, deviations are above 4Å showing instability of the complex for the 100 ns of simulation. RMSD plot suggest that the complex is stable up to 40 ns but it loses its stability onwards. Figure 14(c) represents the RMSF (root mean square fluctuation) curve for the system. RMSF keeps track of changes in each amino acid base pair over the course of the MD simulation, as well as changes in the nucleic acid's flexible areas. High- and low root mean square fluctuations levels, respectively, distinguish loosely bound and tightly bound sections in the DNA strands. The figure gives RMSF curve which represent insignificant fluctuations. Figure 14(d) represents the variations in the radius of gyration for the complex system. To understand the compactness of DNA and the dynamical stability of DNA-ligand complex systems, values of radii of gyration were obtained. These variations in energies were obtained through gmx_gyrate programme inbuilt in GROMACS software suite.

Firstly, all the compounds were optimized for to start the process. Molecular Docking was performed on 25 systems of DNA-ligand. It was observed that most of the compounds bind with DNA as minor groove binders and binds to AT-rich region, except TBBPA. TBBPA intercalates with 1DSC and 2ROU as well as binds in the major groove of 1RMX. Results confirmed that TBBPA binds with DNA with maximum binding energy, it means that the TBBPA-DNA complex formed is most stable amongst all the complexes of BPA derivatives with different types of DNA. The larger size of TBBPA may be the reason for the high binding affinity between the ligand and DNA. TCBPA-DNA complex system has binding energy next to TBBPA-DNA system. Hydrogen bond analysis and hydrophobic bond analysis of each system provides more details about the bonding in each complex. As known from literature, in the case of groove binding, H-bonds were main bonds between the target and the ligand whereas for intercalation, hydrophobic bonding dominates. TBBPA forms maximum hydrophobic bonds with different segments of DNA. As BPS and TBBPA are mostly used as an alternative to BPA, further study was focused on these two compounds. Molecular Dynamics simulations of 100ns was performed for two systems, BPS + 1BNA and TBBPA + 1BNA to for the time dependent study of stability of the system. Best poses of the system obtained from molecular docking having least energy were taken as the input for molecular dynamics simulations. After analysing trajectories obtained from MD simulations, it was confirmed that the BPS + 1BNA complex loses its stability after a few nanoseconds whereas TBBPA + 1BNA sustain stability during the whole time of 100ns. Different graphs showing variation of H-bonds, RMSD curve, RMSF curve and variation in radius of gyration confirmed the stability of the complex with time. For TBBPA-1BNA complex system, all the curves showed insignificant deviations which confirmed the stability of the complex system with time. All the computational tools and techniques combined together predicted the stability of compound TBBPA with DNA. Present study tells that TBBPA interacts with DNA with maximum affinity among all BPA derivatives and this interaction is stable with time, we can conclude that TBBPA compounds which come in the human body may interact with DNA. This study conclude that as TBBPA interacts with DNA strongly as compare to BPA and other derivatives, this compound may be as hazardous as BPA for the human body. As there are very few studies regarding this subject, current chapter provides a base for more explicit and elaborated investigation of this compound theoretically and experimentally.

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The authors declare no competing interests.

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Modeling studies on the Interactions of Endocrine Disruptive Compound BPA and its Analogs with dsDNA

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Abstract

Figures

Introduction

Results and Discussion

Geometry Optimization

Molecular Docking

BPA & its Analogs with 1BNA

BPA & its Analogs with 1DSC

BPA & its Analogs with 1RMX

BPA & its Analogs with 2ROU

BPA & its Analogs with 195D

Hydrogen Bond Interaction Analysis

Hydrophobic Interaction Analysis

Molecular Dynamics

MD results for TBBPA-1BNA complex

MD results for 1BNA-BPS complex

Conclusion

References

Additional Declarations

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