Molecular Modeling Studies of Some Uracil and New Deoxyuridine Derivatives
Molecular modeling results reported in this paper are crucial in highlighting the quantitative relationship between the optimized structure and computed molecular properties related to four newly synthesized uracil derivatives with promising biological potential as anticancer bioactive agents. Moreover, 5-fluorouracil (5-FU) and its tautomers and thiouracils molecular properties are studied and correlated with their biological activities. The great medical importance of these and similar molecular systems requires research on their quantitative structure-activity relationships (QSAR) in order to further improve our knowledge about how receptor binding, selectivity, and pharmacological effects are achieved. Modeling is performed in the ground and the first singlet excited states using density functional theory (DFT) and its time-dependent extension (TD-DFT), respectively.
Uracils are considered as privileged structures in drug discovery with broad topics of biological activities and synthetic accessibility. Antiviral and anti-tumor are the two most widely reported activities of uracil analogs, however, they also exhibit herbicidal, insecticidal and bactericidal activities. Their antiviral potential is based on the inhibition of a key step in viral replication pathway resulting in potent activities against HIV, hepatitis B and C, the herpes viruses, and so forth. Uracil derivatives such as 5-fluorouracil or 5-chlorouracil were the first pharmacological active derivatives to be generated [1–10]. Numerous modifications of uracil structure (see Figure 1) have been performed to tackle toxicity problems resulting in the development of derivatives possessing better pharmacological and pharmacokinetic properties including increased bioactivity, selectivity, metabolic stability, absorption, and lower toxicity. Researches of new uracils and fused uracil derivatives as bioactive agents are related to modifications of substituents at different positions of the pyrimidine ring .
5-Fluorouracil (5-FU) is an antimetabolite of the pyrimidine analog type and a well-known antitumor agent, which has been widely used in the treatment of solid tumors such as colon or breast cancers . Because 5-FU is similar in shape to uracil but does not perform the same chemistry as uracil, the drug inhibits RNA replication enzymes, thereby eliminating RNA synthesis and stopping the growth of cancerous cells. Although 5-FU has had clinical success as a single agent, it has been modified by different ways to synthesize its derivatives, which may improve its therapeutic index because of its well-known side effects such as short half-life, wide distribution, low selectivity, and various toxic side effects. Recently chemists have paid more attention to the conjugates of 5-FU with a wide spectrum of low- or high-molecular-weight carriers (Figure 2). Generally, the introduction of fluorine atoms into organic molecules usually promotes dramatic changes in their biological properties .
Since the target of 5-FU is Thymidylate Synthase (TS), it is of utmost importance to discuss the role of TS enzyme, which catalyzes the conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP) (or 5′-thymidylic acid). It provides the sole de novo pathway for biosynthesis of dTMP (Figure 2). It is worth pointing out, however, that fluorinated FdUMP (2′-deoxy-5-fluorouridine 5′-(dihydrogen phosphate)) is generated by conversion of 5-FU in the body. Because of the central role of TS in the synthesis of an essential DNA precursor and its importance as a chemotherapeutic target, the enzyme has been much studied [14, 15].
Electronic and structural factors thought of as binding requirements of substrates and analogs will be studied because there are several extremely potent inhibitors of TS. 5-Fluorouracil is considered as mechanism-based inhibitor of TS because it forms stable covalent adduct during TS catalytic function .
Thus, we are interested in highlighting the relationship between the optimized structure and chemical properties related to the biological activity of the uracils, predominantly for 5-fluorouracil (5-FU), uracil (U), thiouracils (TU), and dithiouracil (DTU) as well as some new uracil derivatives (5′-aminodeoxyuridines (I), (II), and (III)) and amino acid ester conjugate of 5-FU (IV)  with promising biological potential. Uridine is a glycosylated pyrimidine analog containing uracil attached to a ribose ring (or more specifically. a ribofuranose) via a β-N1-glycosidic bond. Gaussian 09 and Spartan’14 Modeling packages will be applied using density functional theory (DFT) and its time-dependent extension (TD-DFT) [17–21].
Ground- as well as excited-state electronic properties such as optimized geometry parameters and partial atomic charge distribution are obtained for each molecule studied as well as drawings of total electron density mapped with the ESP calculated for surface points only . These drawings provide important visualized information on the molecule as seen by another molecule. Furthermore, reactivity indices (such as chemical potential, global hardness, and softness) of the drug molecules are calculated to map molecular reactivity as inhibitors of Thymidylate Synthase (TS), which plays the central role in the synthesis of an essential DNA precursor, and its importance as a chemotherapeutic target. Furthermore, interaction between 5-FU and the in-body converted form FdUMP will be studied to find out the influence of 5-FU on the reactivity of the substrate FdUMP that enforced TS enzyme to stop functioning.
The theoretical calculations are carried out using Gaussian 09, Gaussian Inc. (USA), quantum chemical package within the framework of DFT and TD-DFT (with 6 MOs taken into account in the CI) and visualized by Gausview05 program. 12- and 6-core pro-MAC computers were used to perform the computations. The geometry optimization of each of the studied molecule was carried out in vacuum as implemented in the Gaussian 09 package . The geometry of a molecule was optimized using the hybrid exchange-correlation B3LYP  functional with the 3-21G basis set, which is a good compromise between accuracy and efficiency. The further expansion of the basis set has less impact on the accuracy of the molecular parameters. We have also used the 6-31+G(d) basis set for some of the studied species and obtained similar results. Therefore, we will report the results obtained from the 3-21G basis set. Basis set 6-31+G(d,p) was used in case of dUMP and FdUMP molecules.
The DFT-B3LYP method has been demonstrated to predict excellent geometries and energies. Vibration frequency calculations were performed to confirm whether the obtained geometry represents a transition or minimum energy structure. The useful reaction field model used for solvation is the conductor-like polarizable continuum model (CPCM), which performs a PCM (polarized continuum model) calculation .
User-friendly Spartan’14 (parallel suite version, Wavefunction, Inc., USA) computational chemistry software was also used to facilitate our computational tasks. DFT-B3LYP with 6-31 basis set was used for studying the interactions between 5-FU and FdUMP.
3. Results and Discussion
3.1. DFT Local Indices for Reactivity and Liability of Electron Density
Local properties are highly desirable in establishing a reactivity-oriented description of molecular systems. Global reactivity indices were estimated according to the equations recommended by Politzer and Murray . In particular, the electronic chemical potentials (), chemical hardness (), and softness () of the inhibitors studied were evaluated in terms of the one-electron energies of the frontier molecular orbital HOMO and LUMO, using the following equations:where and are the energies of the highest occupied and the lowest unoccupied molecular orbitals, HOMO and LUMO, respectively. The chemical potential measures the escaping tendency of electron from equilibrium and the global hardness can be seen as the resistance to charge transfer (or the band gap as has been shown in Figure 3), while softness gives indication of how large is electron transfer to/from the molecule when the chemical potential changes [23–25].
The calculated values are tabulated in Table 1. Escaping tendency of electronic charge -value slightly increases in solvent cage relative to that computed in vacuum and solvent nature is of minor importance. Chemical potential, which measures the escaping tendency of electrons, and is related to molecular electronegativity (−chemical potential; that is, ) decreases in the order DTU > 5-FU > AMINOFU > TU > U > U124OH-COCH3 > U124F > U124OH,whereas hardness decreases in the order 5-FU > U > U124OH > U124OH-COCH3 > U124F > AMINOFU > TU > DTU.Our results are in agreement with the general conclusions that the introduction of fluorine atoms into organic molecules accounts for their remarkable reactivity indices and usually promotes dramatic changes in their biological properties.
The calculated reactivity descriptors listed in Table 1(a) favor least charge transfer liability in case of 5-FU. Electronic and structural factors thought of as binding requirements of substrates and analogs studied could shed light on its role as potent inhibitors of TS. Our results explain why 5-FU is previously considered as mechanism-based inhibitor of TS because it forms stable covalent adduct during TS catalytic function .
Further support comes from the computed Mulliken charges on individual atoms of molecules (see Supplementary Table 1 of the Supplementary Material available online at http://dx.doi.org/10.1155/2016/5134732). Inspection of Supplementary Table 1 (Supplementary Material) reveals generally the following.
(1) Nitrogen and oxygen atoms have the majority of negative charges in all molecules studied, whereas C4 of the uracil ring (tagged 5 in case of 5-FU) has the majority of positive charges.
(2) They increase in charges due to solvation.
(3) The general sequence of decreasing charges on the simple uracils is 5-FU > U > TU > DTU.
And in case of 5′-amino-2′-deoxyuridines and the amino acid ester conjugate of 5-FU (IV) order is I ≥ II > III > IV.
(4) Remarkable charge alternation is observed in case of 5-FU gas phase, whereas solvation induces charge equalization on different atoms.
3.2. Analysis of Mapped Molecular Electrostatic Surface Potential (ESP)
The molecular electrostatic potential surface (ESP) provides a visual method to understand the relative polarity of the compounds [23, 24]. Electrostatic potential surfaces mapped (ESP map) with electron density are shown in Figure 4 and Figure 5 illustrates the charge distributions of the molecule three dimensionally and is very useful in research of molecular structure with its physiochemical property relationship [25–27].
These pictures illustrate an electrostatic potential model of the compounds, computed at the 0.0004 a.u. isodensity surface. ESP maps will be used to determine how molecules interact with one another (see Section 3.3).
3.3. The Interaction between 5-FU and Its 5-Fluoro-2′-deoxyuridine 5′-Monophosphate (FdUMP)
Administered, as the premetabolite, 5-FU is a mechanism-based inhibitor of TS that is used in chemotherapy.
We used Spartan’14 parallel suite (8 threads, 4-core Intel i7-based processor) Mac version to simplify exploration of the effect of 5-FU administered on the FdUMP produced in human body. This has a direct impact on TS suicide substrate leading to a synergistic effect on blocking cell division and replication. Based on the ESP maps, we examined different orientations for steric fit to FdUMP with almost the same results as reflected in the partial atomic charges. We scored each on the basis of the equilibrium geometry minimization as well as the energy of the electrostatic interaction with the substrates of the enzyme. Global reactivity descriptors, chemical potential, hardness, and softness beside partial atomic charges as well as ESP maps of the molecules, are calculated (Tables 2 and 3) and visualized in Figure 6. The interaction between 5-FU and FdUMP results in the following. (1) Two H-bonds form between H2⋯O8 and H22⋯O5 with optimized bond lengths 1.784 and 1.837 . (2) Molecular electronegativity (expressed as increasing chemical potential) increases due to charge transfer from 5-FU part to FdUMP moiety (see HOMO-LUMO charge transfer in Figure 7) concomitant with decrease in global hardness and increase in global softness. Thus, it could be reasonably predicted that these changes should result in more reactive adduct when covalently combined with TS, as suggested by the mechanism of TS function, leading to faster stop action of TS enzyme in producing DNA. As a result, cell division and DNA replication should be remarkably blocked. (3) Atomic charges remarkably changed, in particular, on the interacting sites of the molecular fragments. It is worth pointing out that the nonconverted portions of the 5-FU enhance the reactivity of the converted 5-FU to FdUMP towards the TS enzyme leading to efficient blocking of cell division and DNA replication.
3.4. Tautomers Stabilities
In a previous study  it was confirmed that the diketo tautomer is the most stable form of uracil and its derivatives in a water solution. In solid state 5-FU exists also in the ketonic form . Tables 4(a) and 4(b) and Figure 8 list the all possible tautomers that are generated using Spartan’14 tautomer search and optimized by B3LYP/6-31 model. In agreement with the aforementioned studies, our thermodynamic data indicates the stability of ketonic form (T6) relative to other forms. Examining frontier orbitals reveals that T2 with lowest energy gap is the most reactive form. The least energy and thermodynamically stable T3 that exhibits largest dipole moment shows substantial solvation energy change in aqueous solution.
Reactivity descriptors and electrostatic surface potential mapped onto total electron density (ESP map) of eight uracil derivatives, namely, 5-fluorouracil (5-FU), uracil (U), thiouracils (TU), and dithiouracil (DTU) as well as some new uracil derivatives (5′-aminodeoxyuredines I, II, and III) and amino acid ester conjugate of 5-FU (IV), have been calculated and visualized. The results revealed the following.
(a) Calculated molecular electronegativity (−chemical potential; that is, ) decreases in the order DTU > 5-FU > IV > TU > U > I > III > II.
(b) On the other hand, hardness, which measures the resistance to electron transfer, is closely linked to band gap. It decreases in the order 5-FU > U > II > I > III > IV > TU > DTU.
Our results are in agreement with the general conclusions that the introduction of fluorine atoms into uracil rings accounts for their remarkable reactivity indices and usually promotes dramatic changes in their biological properties.
(c) The calculated reactivity descriptors favor least charge transfer liability in case of 5-FU and the general sequence of decreasing Mulliken charges on the simple uracils is 5-FU > U > TU > DTU.
(d) And in case of 5′-amino-2′-deoxyuridines and the amino acid ester conjugate of 5-FU (IV) order is I ≥ II > III > IV.
(e) Remarkable charge alternation is observed in case of 5-FU gas phase, whereas solvation induces charge equalization on different atoms.
(f) As can be seen from the ESP maps of the studied molecules, while regions having the negative potential are over the oxygen atoms of the uracil part of the molecules; the regions having the zero or small positive potential are over the remaining part. These results provide a visualized recognition tool for the studied molecules, guiding its reactivity towards receptors.
(g) The interaction between 5-FU and FdUMP results in a synergistic effect in blocking cell division and DNA replications.
Finally, amongst the tautomers of 5-FU, the diketo form is the most stable one. Molecular modeling, thus, is accelerating the pace of cancer drug efficiency and discovery.
The authors declare that they have no competing interests.
The computed Mulliken charges on individual atoms of the molecules studied.
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