Quantum Chemical Studies of Anti-Cancer Chemotherapy Drug 4-Amino-1-[(2R,3R,4S,5S)-3,4,5-Trihydroxytetrahydrofuran-2-yl]-1,3,5-Triazin-2(1H)-one (Azacitidine)

I.E. Otuokere and F. J. Amaku

Department of Chemistry, Michael Okpara University of Agriculture, Umudike, Nigeria.

*Corresponding Author E-mail: ifeanyiotuokere@gmail.com

ABSTRACT:

4-amino-1-[(2R,3R,4S,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]-1,3,5-triazin-2(1H)-one (azacitidine) is an anti-cancer chemotherapy drug mainly used in the treatment of myelodysplastic syndrome

 (MDS). Azacitidine is a chemical analogue of the cytosine, a nucleoside found in DNA and RNA. Conformational analysis and geometry optimization of azacitidine was performed according to the Hartree-Fock (HF) calculation method by ArgusLab 4.0.1 software. Molecular mechanics calculations were based on specific interactions within the molecule. These interactions included stretching or compressing of bond beyond their equilibrium lengths and angles, torsional effects of twisting about single bonds, the Vander Waals attractions or repulsions of atoms that came close together, and the electrostatic interactions between partial charges azacitidine due to polar bonds. Surface created to visualize ground state properties as well as excited state properties such as orbital, electron densities, electrostatic potential (ESP) spin densities. The generated grid data were used to make molecular orbital surface, visualized the molecular orbital, electrostatic potential map and electron density surface. The steric energy for azacitidine was calculated to be 0.12162642 a.u.( 76.32179805 kcal/mol). It was concluded that the lowest energy and most stable conformation of azacitidine was 0.12162642 a.u.( 76.32179805 kcal/mol) The most energetically favourable conformation of azacitidine was found to have a heat of formation of 157.6452 kcal/mol. The self-consistent field (SCF) energy was calculated by geometry convergence function using RHF/PM3 method in ArgusLab software. The most feasible position for azacitidine to induce antineoplastic activity in the receptor was found to be -110.6126839099 au (- 69410.5697 kcal/mol)

KEYWORDS: Azacitidine, molecular mechanics, Arguslab software, SCF energy.

INTRODUCTION:

4-amino-1-[(2R,3R,4S,5S)-3,4,5-trihydroxytetra hydrofuran-2-yl]-1,3,5-triazin-2(1H)-one (azacitidine) is an anti-cancer chemotherapy drug mainly used in the treatment of myelodysplastic syndrome (MDS). Azacitidine is a chemical analogue of the cytosine, a nucleoside found in DNA and RNA ^{[1, 2]} . Azacitidine is thought to induce antineoplastic activity via two mechanisms; inhibition of DNA methyltransferase at low doses, causing hypomethylation of DNA, and direct cytotoxicity in abnormal hematopoietic cells in the bone marrow through its incorporation into DNA and RNA at high doses, resulting in cell death ^[3].

As azacitidine is a ribonucleoside, it incorporates into RNA to a larger extent than into DNA. The incorporation into RNA leads to the dissembly of polyribosomes, defective methylation and acceptor function of transfer RNA, and inhibition of the production of protein ^[4,5] . Its incorporation into DNA leads to a covalent binding with DNA methyltransferases, which prevents DNA synthesis and subsequent cytotoxicity ^[6]. Being a ribonucleoside, it has been shown to be effective against HIV ^[7].

Local charges such as Mulliken charges and ZDO charges are also generated from arguslab using the AM1 parameterized method. In the zero deferential overlap (ZDO) approximation, the product of two deferent atomic orbitals is set to zero. The integra which survives the ZDO approximation was partly computed using the uniform charge sphere and the rest parameterized. The result produced is the integrated form of Hückel Theory which takes into account electron repulsion. Mulliken charges arise from the Mulliken population analysis ^{[8, 9]} and provide a means of estimating partial atomic charges from calculations carried out by the methods of computational chemistry, particularly those based on the linear combination of atomic orbitals molecular orbital method, and are routinely used as variables in linear regression (QSAR) procedures ^{[10, 11]}. The molecular mechanics energy expression consists of a simple algebraic equation for the energy of a compound. It does not use a wave function or total electron density. The constants in its equation are obtained either from spectroscopic data or ab initio calculations. A set of equations with their associated constants is called a force field. The fundamental assumption of the molecular mechanics method is the transferability of parameters. In other words, the energy penalty associated with a particular molecular motion. These forces are described by potential energy function of structural features like bond lengths, bond angles and torsion angles etc. The energy (E) of the molecule is calculated as a sum of terms as in equation (1).

E = E stretching + E bending + E torsion + E Vander Waals + E electrostatic + E hydrogen bond + cross term These terms are of importance for the accurate calculation of geometric properties of molecules. The set of energy functions and the corresponding parameters are called a force field ^[12] .

MATERIALS AND METHODS:

The geometric optimization of azacitidine was studied using the window base Arguslab ^[13] and ACD lab ^[14] chemsketch softwares. Azacitidine chemical structure was built using ACDlab chem sketch and saved as MDL molfiles (mol). The azacitidine structure was generated by Argus lab, and minimization was performed with molecular mechanics method ^{[15, 16]} .The minimum potential energy was calculated by using geometry convergence function in Argus software. In order to determine the allowed conformation the contact distance between atoms in adjacent residues examined was using the criteria for minimum Vander Waal contact distance Surface created to visualize ground state properties as well as excited state properties such as orbital, electron densities, electrostatic potential (ESP) spin densities. The generated grid data were used to make molecular orbital surface, visualized the molecular orbital, electrostatic potential map and electron density surface. The minimum potential energy was calculated for drug receptor interaction through the geometry convergence map ^[15,16].

RESULTS AND DISCUSSION:

Prospective view and calculated properties of azacitidine molecule is shown in Figure 1. The active conformation and electron density mapped of azacitidine by ACDlabs-3D viewer software are shown in Figure 2 and 3 respectively. Figure 4 and 5 shows HOMO and LUMO respectively. Figure 6 shows Electrostatic potential of molecular ground state mapped onto the electron density. Atomic coordinates of molecule is given in Table1 and bond length, bond angles, dihedral angles are given in Tables 2, 3 and 4 respectively, which are calculated after geometry optimization of molecule from Arguslab by using molecular mechanics calculation. ZDO and Mulliken atomic charges of azacitidine (Table 5) were determined using PM3 method. Table 6 shows calculated final energy evaluation of azacitidine molecule.

Figure 1: Prospective view of Azacitidine by ACD/ChemSketch

Figure 2: Electron density clouds of Azacitidine by ACDlabs 3D viewer.

Figure 3: Prospective view of active conformation of Azacitidine by Arguslab.

Figure 4: Highest occupied molecular orbital’s of Azacitidine.

Figure 5: Lowest unoccupied molecular orbital’s of Azacitidine.

Figure 6: Electrostatic potential mapped density of Azacitidine.

Figure 7: SCF energy of Azacitidine.

Table 1: Atomic coordinates of Azacitidine.
S.No	Atoms	X	Y		Z
1	C	20.861500	-36.671100		0.000000
2	C	20.861500	-38.001100		0.000000
3	N	19.709600	-36.006100		0.000000
4	N	19.709600	-38.666100		0.000000
5	C	18.557800	-36.671100		0.000000
6	C	18.557800	-38.001100		0.000000
7	C	19.709500	-34.676100		0.000000
8	C	20.861300	-34.011100		0.000000
9	N	20.861300	-32.681100		0.000000
10	C	19.709500	-32.016100		0.000000
11	C	22.013200	-32.016000		0.000000
12	C	19.709500	-30.686000		0.000000
13	C	22.013200	-30.686100		0.000000
14	N	20.861300	-30.021100		0.000000
15	C	22.013200	-34.676100		0.000000
16	O	22.013300	-38.666200		0.000000
17	O	17.406000	-38.666100		0.000000
18	O	23.165000	-30.021100		0.000000
19	O	18.557700	-30.021000		0.000000
20	H	19.709500	-39.996100		0.000000
21	H	20.861300	-28.691100		0.000000
Table 2: Bond length of Azacitidine
Atoms				Bond length
(C1)-(C2)				1.458000
(C1)-(N3)				1.433804
(C2)-(N4)				1.433804
(C2)-(O16)				1.407689
(N3)-(C5)				1.433804
(N3)-(C7)				1.436817
(N4)-(C6)				1.433804
(N4)-(H20)				1.062577
(C5)-(C6)				1.458000
(C)6-(O17)				1.407689
(C7)-(C8)				1.464000
(C8)-(N9)				1.436817
(C8)-(C15)				1.464000
(N9)-(C10)				1.433804
(N9)-(C11)				1.433804
(C10)-(C12)				1.458000
(C11)-(C13)				1.458000
(C12)-(N14)				1.433804
(C12)-(O19)				1.407689
(C13)-(N14)				1.433804
(C13)-(O18)				1.407689
(N14)-(H21)				1.062577

Table 3: Bond angles of Azacitidine
Atoms	Bond angles	Alternate angles
(C2)-(C1)-(N3)	120.000000	257.053574
(C1)-(C2)-(N4)	120.000000	257.053574
(C1)-(C2)-(O16)	120.000000	238.736810
(C5)-(N3)-(C1)	120.000000	198.144139
(C1)-(N3)-(C7)	120.000000	197.520556
(N4)-(C2)-(O16)	120.000000	325.928547
(C2)-(N4)-(C6)	120.000000	198.144139
(C2)-(N4)-(H20)	120.000000	108.672864
(C5)-(N3)-(C7)	120.000000	197.520556
(N3)-(C5)-(C6)	120.000000	257.053574
(N3)-(C7)-(C8)	120.000000	254.659028
(C6)-(N4)-(H20)	120.000000	108.672864
(N4)-(C6)-(C5)	120.000000	257.053574
(N4)-(C6)-(O17)	120.000000	325.928547
(C5)-(C6)-(O17)	120.000000	238.736810
(C7)-(C8)-(N9)	120.000000	254.659028
(C7)-(C8)-(C15)	120.000000	186.134654
(N9)-(C8)-(C15)	120.000000	254.659028
(C8)-(N9)-(C10)	120.000000	197.520556
(C8)-(N9)-(C11)	120.000000	197.520556
(C10)-(N9)-(C11)	120.000000	198.144139
(N9)-(C10)-(C12)	120.000000	257.053574
(N9)-(C11)-(C13)	120.000000	257.053574
(C10)-(C12)-(N14)	120.000000	257.053574
(C10)-(C12)-(O19)	120.000000	238.736810
(C11)-(C13)-(N14)	120.000000	257.053574
(C11)-(C13)-(O18)	120.000000	238.736810
(N14)-(C12)-(O19)	120.000000	325.928547
(C12)-(N14)-(C13)	120.000000	198.144139
(C12)-(N14)-(H21)	120.000000	108.672864
(N14)-(C13)-(O18)	120.000000	325.928547
(C13)-(N14)-(H21)	120.000000	108.672864

Table 4: Dihedral angles of dexrazoxane
Atomic Bonds	Dihedral angles
(N4)-(C2)-(C1)-(N3)	5.000000
(O16)-(C2)-(C1)-(N3)	5.000000
(C2)-(C1)-(N3)-(C5)	5.000000
(C2)-(C1)-(N3)-(C7)	5.000000
(C1)-(C2)-(N4)-(C6)	2.500000
(C1)-(C2)-(N4)-(H20)	2.500000
(C1)-(N3)-(C5)-(C6)	5.000000
(C1)-(N3)-(C7)-(C8)	5.000000
(C6)-(N4)-(C2)-(O16)	2.500000
(H20)-(N4)-(C2)-(O16)	2.500000
(C2)-(N4)-(C6)-(C5)	2.500000
(C2)-(N4)-(C6)-(O17)	2.500000
(C6)-(C5)-(N3)-(C7)	5.000000
(C5)-(N3)-(C7)-(C8)	5.000000
(N3)-(C5)-(C6)-(N4)	5.000000
(N3)-(C5)-(C6)-(O17)	5.000000
(N3)-(C7)-(C8)-(N9)	5.000000
(N3)-(C7)-(C8)-(C15)	5.000000
(C5)-(C6)-(N4)-(H20)	2.500000
(O17)-(C6)-(N4)-(H20)	2.500000
(C7)-(C8)-(N9)-(C10)	2.500000
(C7)-(C8)-(N9)-(C11)	2.500000
(C10)-(N9)-(C8)-(C15)	2.500000
(C11)-(N9)-(C8)-(C15)	2.500000
(C8)-(N9)-(C10)-(C12)	5.000000
(C8)-(N9)-(C11)-(C13)	5.000000
(C12)-(C10)-(N9)-(C11)	5.000000
(C10)-(N9)-(C11)-(C13)	5.000000
(N9)-(C10)-(C12)-(N14)	5.000000
(N9)-(C10)-(C12)-(O19)	5.000000
(N9)-(C11)-(C13)-(N14)	5.000000
(N9)-(C11)-(C13)-(O18)	5.000000
(C10)-(C12)-(N14)-(C13)	2.500000
(C10)-(C12)-(N14)-(H21)	2.500000
(C11)-(C13)-(N14)-(C12)	2.500000
(C11)-(C13)-(N14)-(H21)	2.500000
(C13)-(N14)-(C12)-(O19)	2.500000
(H21)-(N14)-(C12)-(O19)	2.500000
(C12)-(N14)-(C13)-(O18)	2.500000
(H21)-(N14)-(C13)-(O18)	2.500000

Table 5: List of Mulliken Atomic Charges and ZDO Atomic Charges of dexrazoxane
S.No	Atoms	ZDO atomic charges	Mulliken atomic charges
1	C	-4.0000	-4.0001
2	C	-4.0000	-4.0000
3	N	-3.0000	-3.0001
4	N	-3.0000	-3.0000
5	C	-4.0000	-4.0000
6	C	-4.0000	-4.0000
7	C	-3.9980	-4.0075
8	C	-2.0232	-2.0096
9	N	4.9847	5.0233
10	C	3.9967	4.0020
11	C	3.9992	4.0028
12	C	3.9913	4.0069
13	C	4.0000	4.0001
14	N	5.0000	5.0000
15	C	-3.9595	-4.0112
16	O	-2.0000	-2.0000
17	O	-2.0000	-2.0000
18	O	6.0000	6.0000
19	O	4.0089	3.9933
20	H	-1.0000	-1.0000
21	H	1.0000	1.0000

Table 6: Final energy evaluation.
S.No.	Force field	Energy value (au)
1	MM bond (Estr)	0.00210013
2	MM (Ebend)+ (Estr‑bend)	0.05301031
3	MM (Etor)	0.04780800
4	MM ImpTor (Eoop)	0.00000000
5	MM vdW (EVdW)	0.01870797
6	MM coulomb (Eqq)	0.00000000
Total		0.12162642 a.u. ( 76.32179805 kcal/mol)
MM = Molecular mechanics

Arguslab was used to see what happened to the electrons in molecules when it absorbed light. Surfaces were made to explore this fascinating phenomenon. Molecules absorbsed energy in the form of UV/visible light, it made a transition from the ground electronic state to an excited electronic state. The excited and ground states have different distributions of electron density. This property is often valuable and sought after by chemists who are interested in molecules that are useful as dyes, sunscreens, etc ^[13]. The HOMO is localized to the plane of the molecule and is a non-bonding molecular orbital. The LUMO is perpendicular to the plane of the molecule and is a combination of the p_z atomic orbitals. The n -> π^* transition is dominated by the excitation from the HOMO to the LUMO. The positive and negative phases of the orbital are represented by the two colors, the red regions represent an increase in electron density and the blue regions a decrease in electron density. However, these calculations were examined in the ground state and also in vacuum ^[13]. The electrostatic potential is a physical property of a molecule that relates to how a molecule is first “seen” or “felt” by a positive "test" charge at a particular point in space. A distribution of electric charge creates an electric potential in the surrounding space. A positive electric potential means that a positive charge will be repelled in that region of space. A negative electric potential means that a positive charge will be attracted. A portion of a molecule that has a negative electrostatic potential will be susceptible to electrophilic attack – the more negative the better ^[13]. QuickPlot ESP mapped density generates an electrostatic potential map on the total electron density contour of the molecule. The electron density surface depicts locations around the molecule where the electron probability density is equal ^[13]. This gives an idea of the size of the molecule and its susceptibility to electrophilic attack. Electron density surface shows the complete surface with the color map. The surface color reflects the magnitude and polarity of the electrostatic potential. The color map shows the ESP energy (in hartrees) for the various colors. The red end of the spectrum shows regions of highest stability for a positive test charge, magenta/ blue show the regions of least stability for a positive test charge ^[13].These images show that the triple and double bonded end of the molecule is electron rich relative to the single bonded end ^[13].

The self-consistent field (SCF) energy is the average interaction between a given particle and other particles of a quantum-mechanical system consisting of many particles. Beacause the problem of many interacting particles is very complex and has no exact solution; calculations are done by approximate methods. One of the most often used approximated methods of quantum mechanics is based on the interaction of a self-consistent field, which permits the many-particle problem to be reduced to the problem of a single particle moving in the average self-consistent field produced by the other particles ^[17]. The final SCF energy of azacitidine was found to be -110.6126839099- 69410.5697 kcal/mol as calculated by RHF/PM3 method using ArgusLab 4.0.1 suite. It should be noted that the Mulliken charges do not reproduce the electostatic potentials of a molecule very well. Mulliken charges were calculed by determining the electron population of each atom as defined by the basis functions ^[18].The standard heat of formation of a compound is the enthalpy change for the formation of 1 mole of the compound from its constituent elements in their standard states at 1 atmosphere. Its symbol is ΔH_f^θ. The most energetically favourable conformation of azacitidine was found to have a heat of formation of 157.6452 kcal/mol via RHF/PM3. The steric energy calculated for azacitidine was 0.12162642 a.u. (76.32179805 kcal/mol).

CONCLUSION:

Conformational analysis and geometry optimization of azacitidine was performed according to the Hartree-Fock (HF) calculation method by ArgusLab 4.0.1 software. Molecular mechanics calculations were based on specific interactions within the molecule. These interactions included stretching or compressing of bond beyond their equilibrium lengths and angles, torsional effects of twisting about single bonds, the Van der Waals attractions or repulsions of atoms that came close together, and the electrostatic interactions between partial charges in azacitidine due to polar bonds. The steric energy for azacitidine was calculated to be 0.12162642 a.u.( 76.32179805 kcal/mol). It was concluded that the lowest energy and most stable conformation of azacitidine was 0.12162642 a.u. (76.32179805). The most energetically favourable conformation of azacitidine was found to have a heat of formation of 157.6452 kcal/mol. The self-consistent field (SCF) energy was calculated by geometry convergence function using RHF/PM3 method in ArgusLab software. The most feasible position for azacitidine to induce antineoplastic activity in the receptor was found to be -110.6126839099 au (- 69410.5697 kcal/mol).

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Received on 11.08.2015 Modified on 28.08.2015

Accepted on 25.09.2015 ©A&V Publications All right reserved

Res. J. Pharmacognosy & Phytochem. 7(4): Oct-Dec. 2015; Page 203-208

DOI: 10.5958/0975-4385.2015.00031.X