INVESTIGATION OF SOLVATION DYNAMICS AND HYDRATION PATTERN OF SIALIC ACID BY AB INITIO AND DFT METHODHTML Full Text
INVESTIGATION OF SOLVATION DYNAMICS AND HYDRATION PATTERN OF SIALIC ACID BY AB INITIO AND DFT METHOD
Department of Chemistry, Sri Krishna College of Engineering and Technology, Coimbatore - 641008, Tamil Nadu, India.
ABSTRACT: Sialic acid is the active site of neuraminidase virus and it proliferates the infection in the human body by cleaving it from the neuraminidase viral protein. The buried water molecule influences the binding between the ligand and the receptor. Hence, solvation dynamics and hydration pattern of sialic acid needs to be investigated to design the antiviral inhibitor. Cluster continuum solvation analysis reveals that the hydrated structures of sialyate ion are progressive increases as a function of water molecules by explicit solvation method, and this pattern attests the presence of buried water molecules in the hexa hydrated structure. Thus, it confirms the presence of trapped water molecules near the functional site of sialic acid. Hence, it can be considered as a promising candidate for the design of a sialidase antiviral drug.
Solvation energy, Sialic acid, Hydrated structure, Cluster continuum
INTRODUCTION: Water molecule plays a central role in mediating the interaction between ligand and receptor. Hydration of bio-molecular species is of great importance in chemical and biological sciences at the molecular level. The importance of water molecules in protein-ligand interactions has been greatly recognized in the past few years 1. The water molecules stabilize the complex between the protein and ligand by hydrogen bonding, and thereby it attributes to the stability of the overall hydrated structures 2. The water molecule occupies less space than the polar side chains of protein, and also it forms multiple hydrogen bonds with the substrate to improve the binding affinity.
Since most of the biological process occurs in solution, the solvent effect must also be considered to unravel the hydration pattern and hydrogen bonding fashion of the biomolecules 3. Sialic acid has received special attention in solvation dynamics and hydrogen bonding systems because it acts on the action of neuraminidase virus 4. Hydration of sialic acid is one of the most ubiquitous processes in chemical as well as in biological systems. Hence, hydrogen bonding is most widely studied in a vast area of chemical systems, from simple intermolecular interaction to large bio-molecules 5. Structure and dynamics study of recent literature of bio-molecules reveals that the presence of interlocked water molecules in the protein receptor interactions substantially increases the binding affinity of substrate 6 and accounting for a new era in the inhibitor design.
Scientific reports have proved that the water molecule has a unique property, and thus it has a critical impact on the biological activity of DNA, protein, and enzyme catalysis 7.
In addition, the hydrogen bond formed by the interlocked water molecules affects the intramolecular proton transfer in a biological process. On account of this, the theoretical study of hydrogen bonding in a biological system is crucial for a deeper understanding of the protein interactions and enzyme activity; this eventually provides a rationalization of the protein structure and catalytic pathway of the enzymatic reaction 8. In a nutshell, the solvation dynamics and microsolvation pattern provides better insight to develop and design of antiviral inhibitors. Computational chemistry provides a complementary tool to explore the ionic hydrogen bonds in enzymatic reactions and proteins 9. Hence, explicit solvation analysis of proteins and key biological macromolecules will be useful in predicting the internal binding sites of the protein. The explicit solvation analysis is carried out by forming a hydration shell around the sialic acid by the explicit addition of water molecules.
Computational Methods: Solvation plays a cardinal role in a wide variety of the chemical process, especially in ionic systems. In ionic systems, solvent effects have a considerable influence on the rate and equilibrium of chemical reactions. Therefore, theoretical modeling of liquid-phase chemical reaction must include the solvent effect to predict the feasibility of the reactions. To attain this goal, it is inevitable to develop theoretical methods with the capability of predicting accurate values of solvation free energies. The continuum-based solvation models are very impressive, and its simplicity makes this model very fascinating and used extensively for solvation dynamics computation. Sialic acid structure is obtained from the X-Ray crystallographic database PDB 10 code of MW21, and it is further refined by adding hydrogen atoms using the Gaussian suite of programs. The sialic acid, thus obtained, is used for the electronic structure calculations.
Sialic acid on solvation in the water medium becomes sialate anion due to its inherent ionization of acid group, and hence it referred to as sialyate anion hereafter in this study. All the sialyate anionic compounds are optimized using RHF/6-31G(d) level of theory and performed single point energy calculations using the B3LP/6-31G(d) level of theory in the gas phase. The hydrated structures of sialyate anionic compounds are formed by adding water molecules in the vicinity of key functional groups and likewise, monohydrated to hepta hydrated structures are formed by adding one water to sever water molecules. Conductor like polarized continuum model 11 (CPCM) is employed for solvent energy calculation in the solvent phase and water is employed as the solvent for the solvent phase. The solvation energy and gas-phase binding energy of the substrate and its hydrated structures can be calculated by using the following equation (1), (2), and (3).
ΔE(Bind) = Eg(Substrate-Ligand Complex) n – (E(substrate) n+ E(Ligand)g), n=(1-7) …..(1)
ΔG*solv (A±) = ΔG°clust (A±(S)n + ΔG*solv (A±(S)n + n ΔGvap (S) …..(2)
ΔEgp = [Ex-nH2O – Ex – EH2O] n = (1-7) …..(3)
In the above relation, x is the sialyate anion substrate selected for this study, and n is the number of addition of water molecules. The hydrated structures are formed by explicit solvation method 12, and the cluster continuum solvation model is employed for explicit solvation studies 13. Ab initio and DFT calculation of all the hydrated structures have been carried out by using the Gaussian’03 suite of program 14.
RESULTS AND DISCUSSION:
Analysis of Cluster Continuum Solvation Free Energy of Hydrated Structures: The explicit solvation analysis of sialyate anion in the absence of hydration shell provides solvation energy of -76.7 kcal/mol with a charge density of 0.528 on C2 carbon and -0.771 on the O16 endocyclic oxygen atom. The structure of sialyate anion is shown in Fig. 1A. The first water molecule is added in the vicinity of the C4 hydroxyl group of the sialate anion; the added water molecule forms a hydrogen bond with the C4 hydroxyl group and carbonyl oxygen at 2.324Å and 1.926Å. Hence, it acts as a bridge between the C4 hydroxyl group and thus stabilizes the monohydrated structure. Bridging of water molecules in the protein network increases the binding affinity between the substrate and receptor 15. The monohydrated structure of silyate anion provides continuum solvation free energy of -73.5 kcal/mol, and its structure is shown in Fig. 1.
FIG. 1: SIALYATE ANION
The second water molecule is added in the vicinity of the C8 and C9 hydroxyl group of the glycerol side chain. The added water molecule forms two donor hydrogen bonds at 1.766Å and 1.937Å with the neighboring hydroxyl group. The dihydrated structure attains the solvation energy of -70.43 kcal/mol.
The hydration energy of a dihydrated structure is higher than the monohydrated structure, and thus, it signifies that the hydration energy increases with the explicit addition of water molecules 16, and it is shown in Fig. 1B.
The third water molecule is added near the carbonyl oxygen of the amide linkage, and the added water molecule forms an acceptor hydrogen bond with oxygen at 1.875Å. Fig. 1C shows the hydration of the pattern of trihydrated structure. The trihydrated structure provides the cluster continuum solvation free energy of -63.65 kcal/mol, and it is higher than the continuum solvation free energy of dihydrated structure, and hence it nullifies the presence of water in the vicinity of carbonyl oxygen and favors the bulk interaction in solvation dynamics. Bulk interaction usually decreases the solvation energy due to multiple hydrogen-bonding interactions 17.
The fourth water molecule is added in between the C7 and C9 hydroxyl groups of the glycerol side chain of the sialyate anion. The added water molecule forms a hydrogen bridge between two hydroxyl groups by forming acceptor hydrogen bonds at 2.876Å and 2.046Å, and it is shown in Fig. 1D.
The tetra hydrated explicit structure of sialate anion yields solvation energy of -60.84 kcal/mol, and it clearly signifies that cluster continuum solvation free energy progressively increases as a function of the water molecule and invalidates the specific water molecule binding with the sialic acid. The fifth water molecule is added in the vicinity of carboxylate oxygen, and the added fifth water molecule forms an acceptor hydrogen bond with carboxylate oxygen and donor hydrogen bond with the C2 hydroxyl group, and it is shown in the Fig. 1F. The explicit Penta hydrated structure attains continuum solvation free energy of -64.22 kcal/mol, which is higher than the previous tetra hydrated structure. Therefore, the presence of specific binding of water molecule is perhaps present in the vicinity of carboxylate oxygen on account of strong hydrogen bond and attributes water-specific interaction 18. Sixth water molecule is added in the vicinity of carboxylate oxygen, and its structure is shown in Fig. 1G, and it yields higher cluster continuum solvation energy of -61.46 kcal/mol.
The hexa hydrated structure reveals that the increase in the size of the hydration shell drastically increases the solvation energy. Moreover, the dynamics and bonding of water molecule in hexahydrated structure are strong, and so it attains higher continuum solvation energy, and this validates the presence of water molecule near the functional site of carboxylic acid 19.
The final and seventh water molecule is added in the bay space between the C4 hydroxyl group and carboxylate oxygen, and the added seventh water molecule forms hydrogen bridge between C4 hydroxyl and carboxylic group and stabilizes the structures; its structure has been shown in the Fig. 1H.
The bridging of water molecules plays a vital role in charge transfer and electrostatic attractions. The hepta hydrated structure provides a continuum solvation energy of -54.79 kcal/mol. It is clear from Table 1 that the hexa and hepta hydrated structure attain the highest continuum solvation free energy on account of the larger hydration shell and it also due to the hydrogen bonding cooperative effects and electrostatic charge transfer between cooperative hydrated water molecules.
FIG. 2: CONTINUUM SOLVATION FREE ENERGY OF SIALYATE ANION
It further authenticates that the continuum solvation energy progressively increases as a function of explicit water molecules, and this analysis nullifies the presence of specific water molecules in the binding site, perhaps hexa and hepta hydrated structures have entrapped water molecules due to their higher continuum solvation energies and better charge transfer effects. Hence, it can be considered as the potential candidate for the further development of sialidase inhibitors. It is clear from Fig. 2 that the continuum solvation free energy increases progressively with explicit solvation of water molecules.
TABLE 1: CLUSTER CONTINUUM SOLVAION FREE ENERGY OF SIALYATE ANION AND ITS HYDRATED STRUCTURES
|Compounds||Solvation Free Energy HF/ 6-31(g) kcal/mol ΔGsol (CC)||Solvation free energy B3LYP6-31G(d) (kcalmol) ΔGsol (CC)||Charge density on O16 atom||Charge density on C12 atom||r(C2–O16)
Analysis of Gas-Phase Hydration Energy: The analysis of water-binding energy of hydrated structures is carried to explore the frozen water molecule in the protein network. The monohydrated structure obtains gas-phase water binding energy of -13.98 kcal/mol. It appears that monohydrated structures attain low binding energy. The sialate anion dihydrated structure provides binding energy of -26.97 kcal/mol. It seems that binding energy decreases as a function of water molecules. The trihydrate sialyate anion attains binding energy of 42.2 kcal/mol. Invariably all the hydrated structures losses the binding affinity with water molecule on account of the hydrogen bonding cooperative effects. The tetra hydrated structure attains gas-phase water binding energy of -55.88 kcal/mol and attains insignificant affinity due to the poor orientation of water molecules in the hydration shell. Next, the Penta hydrated structure obtains the gas-phase water binding energy of -72.24 kcal/mol and thus lowers binding energy of Penta hydrated structure and which leads to the conclusion that the increase cluster size decreases the binding energy. The hexa hydrated and hepta hydrated structure of sialyate anion attains binding energy of -101.7 and 102.64 kcal/mol.
FIG. 3: BINDING ENERGY AS A FUNCTION OF EXPLICIT WATER MOLECULES
There is a marginal difference is observed between hexa and hepta hydrated structure, and it implies that the explicit addition of water molecules attains limiting value in gas phase binding energy and it is validated in Fig. 3, which clearly depicts that the addition of seventh water molecule has no effect on the binding affinity with sialyate anion. Hence, the addition of water molecules beyond hepta hydrated structure is insignificance.
Analysis of Solvation Free Energy of Hydrated Structures of Sialiate Anion: The sialyate anion provides solvation free energy of -76.7 kcal/mol without hydration sphere. The monohydrated structure of sialate anion provides free solvation energy of -75.72 kcal/mol and it reveals the hydration favors the solvation of sialyate anion. The dihdrated structure of sialyate anion provides solvation free energy of -75.56 kcal/mol, it appears that the monohydrated and dihydrated structure have the identical solvation free energies due to their stereo orientation effect of water molecule. The trihydrated structure attains solvation free energy of -71.14 kcal/mol. The solvation energy of trihdydrated structure is higher than the dihydrated structure, and thereby, it favors the presence of water molecules in the trihydrate functional site. The tetra hydrated structure of sialyate anion yields a solvation energy of -69.93 kcal/mol.
So, it clearly conveys the information that increases in addition of explicit water molecule increases the solvation energy. It is due to the hydrogen cooperative effects caused by the multiple hydrogen bonds formed by the water molecules. The Penta hydrated structure yields solvation free energy of -63.71 kcal/mol. The addition of a fifth water molecule increases solvation free energy and thus promotes the solvation dynamics of sialate anion with its hydration shell.
It is clearly shown in Fig. 4 that the increase in hydration size increases the solvation free energy due to the effective charge transfer between sialyate ion functional site and the explicit water molecules and thereby facilitates the biological interaction. The hexa and hepta hydrated structures attains solvation free energy of -49.98 kcal/mol and -54.79 kcal/mol, this data clearly signifies that salvation progressively increases as a function of water molecules.
Especially, hexa hydrated structure attains high solvation energy. The solvation dynamics of hexa hydrated structure has a better orientation to favor the intermolecular interaction and charge transfer between the ligand substrate complexes.
The effective charge transfer between the ligand and substrate complex paved the way for the efficient design of antiviral sialidase inhibitors.
FIG. 4: SOLVATION FREE ENERGY OF HYDRATED STRUCTURES OF SIALYATE ANION
TABLE 2: SOLVATION FREE ENERGY AND GAS PHASE BINDING ENERGY OF SIALYATE ANION HYDRATED STRUCTURES
|Compounds||Solvation free energy (kcal/mol) HF/6-31(g) ΔGsol||Solvation free energy B3LYP6-31G(d) (kcalmol) ΔGsol||Gas-phase water binding energy (kcal/mol) HF/6-31(g)||Gas-phase water binding energy (kcal/mol) B3LYP 6-31G(d)|
CONCLUSION: Ab initio and DFT investigation of solvation dynamics and hydration pattern of sialic acid reveals that the cluster continuum solvation energy progressively increases as a function of water molecules by explicit solvation method. It further reveals that the specific binding of water molecules might be present in the tri hydrated and tetra hydrated structures. Hence, the solvation dynamics should be further explored in trihydrated and tetra hydrated structures, and these compounds are recommended for the design of neuraminidase antiviral drugs. The analysis of gas-phase hydration of explicit water molecules reveals that the binding energy of water molecules in the gas phase drastically decreases as a function of water molecules. The hydrogen-bonded network in the gas phase is not strong to produce hydrogen cooperative effects, and as a result, the hydration decreases as a function of water molecules.
Finally, the analysis of solvation free energy of hydrated structures of sialyate anion discloses that the solvation free energy of explicit hydrated structure increases progressively as a function of water molecules. Hence, it reveals that the hydrogen bonding cooperative effects and ionic interactions are very strong in solvation phenomena. The solvation dynamics of hexa hydrated structure is very impressive because it provides higher solvation energy and thus, it indicates the presence of water molecules trapped inside the functional site of sialate anion. Hence, the microsolvation investigation concludes that the tetra hydrated, penta hydrated, and hexa hydrated structure can be considered for further analysis of design and development of sialidase antiviral drugs.
CONFLICTS OF INTEREST: Nil
- Shridhar RG and Anant DK: Molecular electrostatics for exploring hydration patterns of molecules 2 – Formamide. Ind J Chem 2000; 39A: 50-59.
- Caterina B, Justine T, Russel V and Jonathan EW: Classification of water molecules in protein binding sites. J Am Chem Soc 2007; 129: 2577-87.
- Bhat TN, Bentley GA, Boulot G and Greene MI: Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc Natl Acad Sci U.S.A 1994; 91(3): 1089-93.
- Jianzhi G, Wenfang XU and Jie Z: Structure and functions of influenza virus neuraminidase. Curr Med Chem 2007; 14(1): 113-22.
- Kryachko ES: Water cluster approach to study hydrogen‐bonded pattern in liquid water. Int J Quan Chem 1998; 70(4-5): 831-35.
- Peter GJ: Short range strong hydrogen bonds can they explain enzymatic catalysis. Ch & Bio 1996; 3(3): 163-70.
- Stacey DW, Robyn S, David MS and Radom LA: Theoretical investigation of the effects of electronegative substitution on the strength of C−H•••N Hydrogen Bonds. J Phys Chem A 2001; 105(38): 8718-726.
- Bing G, Thomas W, Michael T and Bowers T: Hydration of protonated aromatic amino acids. J Am Chem Soc 2009; 131(13): 4695-01.
- Grabowski I, Hirata S, Ivanov S and Bartlett RJ: Ab initio density functional theory: OEP-MBPT(2). A new orbital-dependent correlation functional. J Chem Phys 2002; 116(11): 4415-19.
- Garman E and Laver G: Controlling influenza by inhibi-ting the virus neuraminidase. Cu dr tar 2004; 5(2): 119-36.
- Onsager L: Electric Moments of Molecules in Liquids. J Am Chem Soc 1936; 58(8): 1486-93.
- Florian J, Warshel AJ and Langevin A: dipoles model for ab initio calculations of chemical processes in solution: parametrization and application to hydration free energies of neutral and ionic solutes and conformational analysis in aqueous solution. J Phys Chem B 1997; 101(30): 5583-96.
- Cramer CJ and Truhlar DG: Implicit solvation models: equilibria, structure, spectra and dynamics. Chem Revs 1999; 99(8): 2161-200.
- Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann E, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomas J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Salvador P, Dannenberg JJ, Malick DK, Rabuck AD, Raghavachari K, Foresman JB Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Hallacombe MC, Gill MW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, and Pople, JA: Gaussian, Inc., Pittsburgh PA, USA 2001.
- Ataei S, Mehrpouya M and Nili-Ahmadabadi A: Potential drug interactions with cholinesterase inhibitors in Alzheimer patients. Journal of Applied Pharmaceutical Science 2017; 7(01): 223-26.
- Zahraa T, Khudhair and Al-Tamimi EO: Synthesis, identification, theoretical study and effect of 1,3,4-oxadiazole compounds substituted on creatinine ring on the activity of some transfers enzymes. Research J Pharm and Tech 2019; 12(8): 3581-88.
- Yang Y, Cao L, Gao H, Wu Y, Wang Y, Fang F, Tianlong, Lan Z and Rao LY: Discovery, Optimization, and Target Identification of Novel Potent Broad-Spectrum Antiviral Inhibitors. J Med Chem 2019; 62(8): 4056-73.
- Pu SY, Wouters R, SchorJef S, Rina R, Bentov B, Laura I, Cecilia MP and Brien: Optimization of Isothiazolo [4,3-b]pyridine-based inhibitors of Cyclin G associated kinase (GAK) with broad-spectrum antiviral activity. J Med Chem 2018; 61(14): 6178-92.
- Bilkiss BI and Gilles HP: Accuracy and precision of simulated free energies: water permeation of hydrated structures. Mol Sim 2019; 45(5): 466-73.
How to cite this article:
Chandrasekaran K: Investigation of solvation dynamics and hydration pattern of sialic acid by ab initio and DFT method. Int J Pharm Sci & Res 2020; 11(5): 2482-88. doi: 10.13040/IJPSR.0975-8232.11(5).2482-88.
All © 2013 are reserved by the International Journal of Pharmaceutical Sciences and Research. This Journal licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
Department of Chemistry, Sri Krishna College of Engineering and Technology, Coimbatore, Tamil Nadu, India.
15 May 2019
10 December 2019
21 February 2020
01 May 2020