During the last two decades several variants of coronaviruses have caused serious health threats to humanity[1–7]. Among them, severe acute respiratory syndrome coronavirus (SARS-CoV), in 2003 [1–2], Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 [3], porcine epidemic diarrhea coronavirus in 2013 [4], and finally the 2019novelcoronavirus, COVID-19, (officially known as SARS-CoV-2). COVID-19 is a newly emerged human infectious coronavirus that was originated in Wuhan seafood market and quickly spread beyond China [5–6]. In general, coronaviruses cause widespread respiratory and central nervous system diseases in humans [7–9]. Coronaviruses can adapt to new environments through mutation and recombination with relative ease and hence are programmed to alter host range and tissue tropism efficiently [10–11]. The World Health Organization (WHO) has declared COVID-19as a pandemic in March 2020. Up to date over 105 million cases have been reported worldwide, and more than two million casualties. Very recently the U.S. Food and Drug Administration (FDA) has approved two antiviral vaccines against SARS-CoV-2. The first one is due to the Pfizer and BioNTech, while the other one is due to Moderna. Both vaccines have shown a 95% efficiency against this pandemic virus [23].
Although many resent statistical surveys and clinical tests are being rushing on COVID-19 across the globe [12, 13], yet no clue from the available clinical controlled
tests has proven that it may enhances the therapy conclusions about the patients end results [14]. As the pandemic escalate s, it is an essential issue to discover a exceptional therapeutic for COVID-19, and vaccines pledge to different variants of SARS-CoV-2 proteins. This protein types are a family of a mono-stranded enveloped positive-sense RNA virus [15]. The entire RNA sequencing genome procedure revealed that such stranded-RNA is recognized by 29,881 bp while encoding 9860 amino acids (GeneBank no. MN908947) [16]. Moreover, these specific coronavirus proteins via gene fragmentation method uncovers there structural and nonstructural secondary conformations. In particular, SARS-CoV-2 virus encompasses four distinct
structural proteins: Spike, Nucleocapsid, Envelope and Membrane protein [17]. Amongst them, the Spike (S-) glycoprotein is a giant, transmembrane and multifunctional protein. This S-protein compete with other coronavirus proteins by mediating itself in an deadly and vital role with respect to host cell via viral attachment, fusion and entry into it [17,18]. The S-protein has two sub-domains namely, S1 and S2 [19, 20], which are then fissure into various biologically active subunits. Of interest, the S1-subunit which runs the binding to the host cell receptor which finally fascinating the cell entry [19,20]. On the other hand, the whole virus initiation and fusion entry into the host cellular membrane is governed by the S2 portion of the spike protein. During this process the viral contains of the virus is being injected into the infected cell [21, 22]. Furthermore, It has been recently concluded that the coronaviruses adapted the circumvention method to trick the host immune system of the infected host cells using conformational masking and glycan shielding of its own S-protein[22].
Several physical and chemical techniques [28, 29] have been applied to inactivate the virus. Such techniques include heating, UV light and ionizing radiation methods. Each rout has its own drawback regarding epitopes damage and development during medical treatment. Gamma irradiation might be considered as a very safe and effective method as indicated in many recent research articles (for full review see [28] and the references therein). On the other hand, the electromagnetic (EM) spectrum between the UV (i.e., 1018 Hz) and the X-ray radiation (i.e., 1019 Hz) is very sensitive to molecular vibration between groups of atoms in macromolecules [30]. Since the resonance absorption energy depends on the protein backbone molecular structure of the amino acids, then each molecule produces its own vibration resonance frequency signature which may lead to the breaking up of the protein structure at specific position along its backbone [31, 32].
Many researchers have employed the five-parameter geometric progression (G-P) fitting method which is originally developed and pioneered by Berger and Hubbell [24] to determine both EABF and EBF for amino acids, single-chain fatty acids and carbohydrates and other non-biological compounds [25]. These studies have shown that G-P fitting is a convenient method for estimating the energy absorption and exposure buildup factors (i.e., EABF and EBF) for many biological molecules. These two important factors may be used to pinpoint the resonance frequency or energy of the viral RNA or DNA strand. Scanning the energy range from few keV up to hundreds of keV may enable the determination of the breaking-up energy of specific sub-domains of the protein in the target.
Large volume of publications has appeared in literature as a consequence of the development of WinXCom software. Manohara and Hanagodimth [26] in couples of independent research reports have determined the effective atomic numbers and electron densities of some essential amino acids in a broad range of photon energies from a few keVup to 100 GeV. A progressive investigation has also been performed by Kurudireket al. [27] who investigated the effect of γ-ray energy on some important human tissues by calculating the absorption and exposure buildup factors. On further attempt of the same research group, Kurudirek and Onara [28] have detailed the γ-ray energy absorption (EABF) and exposure buildup factors (EBF) for different biological-related molecules in the energy range E∈ [15-1500] keV up to a 40 mfp. Most of these "in vitro" experiments have been performed to understand what is happing at sub-cellular level when X- or γ-ray interacts with proteins, tissues, or cell membrane [29].
In the present work, we are motivated by the current research work onCOVID-19 vaccination development around the globe using the conventional clinical treatment. The roles of the SARS-CoV-2 spike glycoprotein in receptor binding and membrane fusion make it an ideal target for vaccine and antiviral development. The development of SARS vaccines based on the spike protein has been summarized in [33–37]. Here, we propose a novel approach to inhabit the S-protein from entering the host cell by applying UV and X-ray irradiation. Thereby, we have investigated theoretically the effect of photon irradiation on the amino acids building blocks in the SARS-CoV-2 spike protein (see Schematic 1) for possible inhabitation of virus to enter and relocate itself into the host cell. This approach is based on the resonance energy for S2-subdomain of the spike protein to break it up into small fragments (see schematic 1) [18–20]. The molecular formula of the nucleotide bases of S2 protein from different coronaviruses mutations used in this study are summarized in Table 1.