NMR Shielding and S-NICS Investigation for Imipenem, Penicillin G, Ticarcillin, Ampicillin and Clavulanic Acid in View point of Bio-Nanotechnology

Introduction

Antibiotics are molecules that stop or kill the growth of, microorganisms, including both bacteria and fungus. Antibiotic that block the growth of bacteria is called bacteriostatic” and antibiotic that kill bacteria is called “bactericidal.

Antibiotic is specific chemical substance produced (or derived) by living organisms that are capable of inhibiting the life processes of other organisms^1-10.

A test, resulting in the classification of bacteria, has developed by “Hans Christian Gram” (a Danish microbiologist) including gram(+) bacteria and gram(-) bacteria.

Currently there are several classifications of antibiotics which can be summarized as various groups such as  (1)-Benzyl-penicillins which are including Penicillin G, benzyl-penicillin sodium, procaine benzyl-penicillin, benzathine penicillin (2)- anti-staphylococcal penicillins (3)- Phenoxy-penicillins including Penicillin V and Propicillin Oxacillin, Dicloxacillin and Flucloxacillin (4)- Quinolones including Group(I): Norfloxacin Group(II): Enoxacin, Norfloxacin, Ciprofloxacin, Group(III): Levofloxacin, Group(IV): Moxifloxacin (5)-ß-Lactam/ß-lactamase inhibitor including Ampicillin^1-5, Amoxicillin^3-5, Mezlocillin^2-4, Piperacillin, Ampicillin/sulbactam^3-6, Amoxicillin / clavulanate,  Piperacillin/ tazobactam and Sulbactam in free combinations^4-7 (6)- Cephalosporins including Cefotaxime^4-7, Ceftriaxone, Ceftazidime, Cefepime, Cefixime^3-7, Cefpodoxime proxetil^4-8, Ceftibuten (oral) (7)- Azol derivatives including Miconazole, Ketoconazole, Fluconazole, Itraconazole, Voriconazole, Posaconazole (8)- Macrolides including Erythromycin, Spiramycin, Roxithromycin^5-9, Clarithromycin, Azithromycin (9)- Echinocandins including Caspofungin, Anidulafungin, Micafungin (10)- Aminoglycosides including Streptomycin, Gentamicin, Tobramycin, Netilmicin, Amikacin^1-10

Antibiotics are special chemical substances isolated or produced from by living organisms that are able for inhibiting the life activities of other organisms. The first antibiotics were derived from micro-organisms” but currently some are obtained through higher plants and animals. Over 3,000 antibiotics have been synthesized and classified but only a few dozen are used as medicine.

As an example penicillins which has been discovered by Alexander Fleming in 1928, is a kind of antibiotic that has been used in the treatment towards bacteria invasion. Fleming who works at St. Mary’s Hospital London^6-10, left for his holidays therefor left the culture of the microbe near the window of his lab then after he came back, he found an unusual phenomenon of the culture (of microbe) that he had left^1-10.

In the past years (decades), pharmaceutical antibiotic was recognized and sensitized as emerging soil pollutants^11-13. Compounds such as sulfonamides and tetra-cyclins reach agricultural land mostly via infected dung from medicated chattels used as muck. Pharmaceutical antibiotics^5-11 are a large group that comprise mostly ionize and polar able compounds. Hence, their soil adsorption behavior swerved from hydrophobic organic pollutants. furthermore to hydrophobic” interaction, antibiotic may sorb to soils through van der Waals forces, hydrogen bonding, ion or cation exchange and  bridging, finally surface complexes^1-10 .

However, sorption can be overcome by investigating either separated natural soil constituents such as “humic” acid or polymers from well-defined “phenolic” compounds, representing specific site and functionality of “humic” substances that can serve as a model to elucidate mode of binding. “Phenolic” compound is a major building block of “humic” polymer and was found to polymerize to humus-like substance^5-10 .

Penicillin attaches such as penicillin binding protein and interfere with the last step of bacterial cell-wall synthesis which is trans-peptidation or cross linkage by inhibition of transpeptidase and production of autolysin leads to bactericidal action. The mechanism of action for various antibiotics is different.  In view point of bacterial spectrum several points are important such as in effective against organism devoid of peptidoglycan can such as mycobacteria, effective against active organism which synthesizes peptidoglycan cell wall, fungi, viruses and protozoa.  Gram positive organisms have cell wall easily traversed by penicillins and therefore they are susceptible to penicillins, several Gram negative organisms have “porin” permit transmembrane entry of penicillin and so they are susceptible organisms. Staphylococci developed resistance to natural Dicloxacillin, penicillin G and Methicillin which are penicillinase resistance preparations are effective against staphylococci. Combination of penicillins and aminoglycosides has synergistic effect while in view point of absorption; most of them are poorly absorbed after oral administration except amoxicillin and ampicillin. Penicillinase resistant preparation should be given one hour before meals because their absorptions are delayed by presence of food^10-20.

Van der Waals forces and multiple weak H-bonds between zeolites and antibiotics are responsible for the ir-reversible extraction from water of all the examined drugs. Lastly, the most stable tautomer form of each antibiotics adsorbed into the zeolites were identified.

As an instant and important antibiotic it can be mentioned the sulfonamide which is commonly used drug in primary care practice. Reaction to Sulfonamide Antibiotic (SA) is relatively common as compared to other antimicrobials^20-30 .

The hypersensitivities reaction, consisting of fever and non-urticarial rash, usually develop seven up to fourteen days after the medication initiation. The term “sulfa” refers to a derivative of an antimicrobial agent, “sulfanilamide”.

Penicillin was the first antibiotic discovered from natural products (Penicillium). It is a “beta-lactam-antibiotic” that is a part of the amino-penicillin” family and is hastily equivalent to successor, amoxicillin in its spectrum and level of activity which is produced by Penicillium chrysogenum^10-12. Phenylacetic acid for PenicillinG or phenoxyacetic” acid for PenicillinV is used for the larger scale production. Other penicillins are produced semi-synthetically”. Penicillin is primarily specific against gram(+) bacteria because of its higher percentage of peptidoglycan in the cell wall of that organism.

Ampicillin belongs to the penicillin group of β-lactam antibiotics, ampicillins are able to penetrate gram(+) and some Gram(-) bacteria. Ampicillins are semi synthetic penicillins with an extera amino-chain synthesized into the penicillin molecules.

Imipenem is intravenous β-lactam antibiotics discovered which is the first member of the carba-penem” classes of antibiotic. Carba-penems are highly resistant to the β-lactamase enzymes produced by many multiple drug resistant grams(-) bacteria, thus play a key role in the treatment of infection not readily treated with other antibiotics^20-30.

Based on previous works we have modeled and simulated drug delivery systems of those antibiotics^30-88 .In this work we have exhibited the especial properties of Ampicillin, Clavulanic acid, Imipenem, Penicillin G and Ticarcillin in view point of NMR shielding and S-NICS methods for delivering in cell body via QM/MM and Abinitio methods.

Theoretical back ground

NMR Shielding and S-NICS method

There are not theoretically or mathematically reports for the statistical approaches in NMR shielding and nucleus-independent-chemical-shift (S-NICS), Since the asymmetry(η) and skew(κ) parameters have fluctuated in a short distances and in contrast are alternative in long distances.

In the item of axially-symmetric tensor, the σ₂₂ is the same value of σ11 or σ₃₃, and then skew is κ=±1. Through changing the asymmetry between 0≤ η ≤+1 skew is changed between -1≤ κ ≤+1 , and  the parameter “κ” is zero when σ₂₂ = σ_iso.

We have investigated a statistical method via computing of nucleus-independent-chemical-shift (S-NICS) in view point of probes motions in a sphere of de-shielding and shielding spaces of hereto rings in some antibiotics. The reduced anisotropy defined as

Anisotropy (Δσ ) with relation of

including shielding asymmetry (η) is defined as

and

In several items of the axially symmetric tensor

is zero and hence η = 0. However, the asymmetry (η) parameter indicates that how much of the line deviates from an axially- symmetric-tensor, therefore, (0 ≤ η ≤ +1).

The tensor of shielding is interpreted as the sum of an anti-symmetric with the symmetric, and terms (scalar), which are ranks {2- 0 t} tensors which defined as:

The total chemical-shielding-tensors {r} are non-symmetric tensors that can be decomposed into 3 independent tensors as: (1) a traceless symmetric component, (2) an isotropic component, and (3) The traceless component (anti-symmetric). In a spherical representation of tensor, Haeberlen has pointed a fundamental level tensor is better represented in the spherical presentation, so a general second-order property of “σ” may be written as  ,

where the number in brackets indicates to tensor ranks. Spherical tensor is involved in considering the effects of tensor quantities in the density matrix , so using of those representations are inevitable for such study. It is notable that:

and

The component of the shielding tensors have symmetric tensor elements with r_ij = r_ji. These tensors are responsible for a relaxation (CSA) most often illustrated in the literature and can be diagonalized through the rotation onto the shielding tensors of the principal coordinate system.

With a statistical calculation it has been exhibited that a time independent average of (Ω^*) can be remodeled for all above sum of anti-symmetric, asymmetric, and the scalar term, which are rank tensors equal  1, 2 and zero respectively. These methods are based on of a probe with random motions in the de-shielding and shielding spaces of the aromatic rings and anti-aromatic molecules. The magnetics media of spin are seldom isotropic. Therefore, are represented through of span tensor:

and

In the notation of Herzfeld-Berger, tensors have explained with 3 parameters, which they are a combination of the major components in this standard notation. These are including, (Ω), which indicates of a maximum width, (Ω ≥ 0), and (κ) tensors which are a magnitude of this value.

The accurate formulation of (Ω), including the factor of (1-σ_ref) have been described by

Ω = (σ₃₃– σ₁₁) (1-σ_ref)             (10).

Moreover the orientation of a-symmetry tensors are given by

( ; (-1 ≤ κ ≤ +1), and dependent to the position of σ₂₂ with consideration of σ_iso, the sign of κ is either negative or positive.

In the items of the axially symmetric tensors, σ₂₂ equals either σ₁₁ or σ₃₃ and κ= ±1 therefore a = Ω/3, and then parameter “a” and “κ” are equal to zero when σ₂₂ = σ_iso and the parameter “μ” used with the Herzfeld-Berger is dependent to the span of a tensor.

and p² is defined by:

Where

and

correspond to the correlation times for isotropic tumbling and small-step molecular rotation, respectively and in the case of axial symmetry or for isotropic

Density and Energy of Electrons

The electron densities have been illustrated as

Where η_i  is occupation number of orbital (i), φ is orbital wave function, is basis function and C is coefficient matrix, the element of i_th row j_th column corresponds to the expansion coefficient of orbital j respect to basis function i. Atomic unit for electron density can be explicitly written as
e/Bohr³

The relationships between

and valence shell electron pair repulsion have been built by Bader^90,91.The kinetic energies density are not uniquely defined, since the expected value of kinetic energies operator

can be recuperated by integrating kinetic energies density from alternative definition and has been explained as:

The Lagrangian kinetic energy density, “G(r)” is also known as positive definite kinetic energy density.

K(r) and G(r) are directly related by Laplacian of electron density

Becke and Edgecombe noted that spherically averaged like-spin conditional pair probability has direct correlation with the Fermi hole and then suggested electron localization function

Where

and

for close-shell system, since

D and D0 terms can be simplified as

LOL or Localized orbital locator is another item for locating high localization regions likewise ELF, defined by Schmider and Becke^89-91.

Where

In all calculations the default gauges-including atomic orbital (GIAO) orbitals were used to obtain molecular magnetic susceptibilities, NMR shielding with Gaussian program.

Computational details

Calculations were accomplished using Gaussian and GAMESS-US packages. The ONIOM method containing three levels from high (H), medium (M), and low (L) calculations have been accomplished in this study. The “advanced DFT” methods are used for high layer of the model and semi-empirical method of Pm6” including pseudo=lanl2 and Pm3MM” are used for the low and medium layers, respectively. There are various situations of non-covalent interaction in this system between hydrogen diffused. In this study, we have mainly focused on getting the optimized results for each item from “advanced DFT” methods including the “m06” and “m06-L”. The “m062x”, “m06-L”, and “m06-HF” are a novel Meta hybrid DFT functional with a good correspondence in non-bonded calculations.

The charge calculation based on molecular-electrostatic-potential or MESP fitting are not well-suited for treating larger systems whereas some of the innermost atoms are located far away from the points at which the MESP is computed. The MESP charge was also calculated using the Merz-Kollman-Singh chelpG^92-96.

The representative atomic charges should be computed as expection values over several molecular positions. The electron densities have been calculated, values of orbital wave-functions, electron spin densities, electrostatic potentials from nuclear / atomic charges, electron localization functions (ELF), localized orbital locators,  total electrostatic potentials (ESP) and the exchange-correlation densities, correlation hole and correlation factors, Average local ionization energies using Multifunctional Wave-function analyzer^89-91.

The contour line map has drawn via Multiwfn software^89-91. The relief map has used to present the height value at every point. The graphs are shown on interactive interface. Shaded surface map and shaded surface map with projection are used in our representation of height value at each situation^89-91 .

Result and Discussion

Three steps have been investigated in this study, first (1), set up a molecule with appropriate starting geometries and second (2) choose a calculation method and its associated choices. Third (3) choose the types of calculations with the relevant options. The Monte Carlo simulations always detect the so-called “important-phase-space” regions which are of low energyies.

In this work, difference in force field has illustrated by comparing the energies calculated by using force fields, Amber, MM+, and OPLS. Also, we have investigated polar solvent and the temperature effects on the stability of antibiotics to CFA (or CGA) in various solvents. The quantum mechanics (QM) calculations were carried out with the HyperChem 8.0 program. This study mainly focuses on the electron density Ampicillin, Clavulanic acid, Imipenem, Penicillin G and Ticarcillin in viewpoint of S-NICS method. The models and situation of molecular structures and binding interaction are shown in figs1- 7. As it is indicated in tables 1-3, the NMR parameters including isotropy, anisotropy, asymmetry, span and S-NICS value have been simulated.

Figure 1: Ampicillin, Clavulanic acid, imipenem, Penicillin G and Ticarcillin structures Click here to View figure

 

Figure 2: Proton and Carbon NMR of Ticarcillin   Click here to View figure

 

Figure 3: Proton and Carbon NMR of Clavuanic acid   Click here to View figure

 

Figure 4: the optimized oriental and iso-surface Hamiltonian kinetic energy for Ticarcillin Versus Z, Y and X-axis   Click here to View figure

 

Figure 5: Gradient map of LOL and ELF for Imipenem in gas phase   Click here to View figure

 

Figure 6: Shaded surface map of LOL for ticarcillin in water   Click here to View figure

 

The fermi hole is a six-dimension function and as a result, it is difficult to be studied visually. Based those equations, Becke and Edgecombe noted that the Fermi hole is a spherical average of the spin which is in good agreement with our results in tables and Figs.

Figure 7: The LOL curves of ticarcillin in water   Click here to View figure

 

According to the equations 16- 22 the largest electron localization is located on atoms which are bonded to nanotubes where the electron motion is more likely to be confined within that region. If electrons are completely localized in those atoms, they can be distinguished from the ones outside. As shown the large density is close to the bonded atoms. The regions with large electron localization need to have large magnitudes of Fermi-hole integration which would lead those atoms towards superparamagnetic.

Conclusion

Once a compound that fulfills all of these requirements has been identified, it will begin the process of drug development prior to clinical trials. Modern drug discovery involves the identification of screening hits, medicinal chemistry and optimization of those hits to increase some properties. One or more of these steps may involve computer-aided drug design. A fascinating result of the theoretical analysis of antibiotics- S-NICS methods were the stable model for drug delivery.

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