Determination the BinDing aBility of n-acetyl cysteine anD its Derivatives with sars-cov-2 main Protease Using molecUlar Docking anD molecUlar Dynamics stUDies

N-acetyl cysteine (NAC) drug has been used as an antioxidant and anti-inflammatory agent in clinical practice and more recently in the treatment of CoVId-19 patients. Using docking analysis and molecular dynamics studies we compare the interaction between of N-acetyl cysteine and its derivatives with SArS-CoV-2 main protease (M pro ) which is essential for processing the proteins translated from the viral rNA. the results obtained from this study showed that NAC benzyl ester (NACBn), NAC ethyl ester (NACet) and NAC amide (NACA) could bind with SA rS-CoV-2 protease better than NAC drug.

C oronaviruses are a diverse category of viruses that infect both humans and some species of animals. These viruses are capable of causing human respiratory infections that are moderate to severe. Furthermore, the recent medical investigations showed that modern coronavirus disease  is triggered by the virus (SARS-CoV-2) causing a multisystem organ dysfunction correlated with severe morbidity and mortality in human [1,2]. Two extremely pathogenic zoonotic coronaviruses, Acute Respiratory Infection Coronavirus Syndrome (SARS-CoV) and Middle East Respiratory Coronavirus Syndrome (MERS-CoV), emerged in humans in 2002 and 2012 respectively, resulted in deadly respiratory diseases [10]. In Wuhan Area, China, a new coronavirus identified as SARS-CoV-2 emerged at the end of 2019, triggering an outbreak of unusual viral pneumonia. This novel coronavirus outbreak, COVID-19, has spread widely around the world as a highly communicable disease [3,4]. Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing global health emergency. The 2019-nCoV causes an ongoing outbreak of lower respiratory tract disease called novel coronavirus pneumonia (NCP) by the Chinese government initially. The World Health Organization finally recommended describing the disease as COVID-19. In the meantime, the International Commission on Virus Taxonomy renamed the 2019-nCoV to SARS-CoV-2. At the end of January 2020, WHO announced COVID-19 as an international health crisis. On 24 February 2020 over than 80.000 cases were reported which included more than 2,700 deaths that affected at least 37 countries around award. Viruses such as SARS-CoV, SARS-CoV PC4-227, and SARSr-CoV-btKY72 were included in the SARS-CoV genus. The newer part of this viral genus is SARS-CoV-2. SARS in the description of SARS-CoV-2, is an expansion of the taxonomy of viruses of SARS genus, rather than the name of SARS disease. In this species SARS is mainly related to its taxonomic association with this species establishing virus, SARS-CoV. In other words SARS can be referred to as a virus in this genus irrespective of whether or not SARS-like diseases are caused [5]. In addition to seasonal influenza, reported pathogens of pneumonia include adenovirus, coronavirus 229E/NL63/OC43, human doi: https://doi.org/10.15407/ubj93.05.043 bocavirus, human metapneumovirus, parainfluenza virus 1/2/3, rhinovirus and respiratory syncytial virus A/B 2 [6,7]. Moreover, these viruses can cause co-infection in the setting of community-acquired bacterial pneumonia [8]. Awareness of the function of these viruses in pneumonic disease has achieved considerable progress using molecular methods [9,10]. A positive sensory, one-strain RNA virus of the genus Betacoronavirus 2 has been found to be a SARS COV-2 [11,12]. Phylogenetic research found that SARS-CoV-2 was closely linked to two SARS-like bat viruses, namely, bat-SL-CovZC45 (GenBank accession no. MG772933.1) and bat-SL-CovZXC21 (GenBank accession no. MG772934.1), but more far away from SARS-CoV (~79 percent similarity), and Middle East respiratory syndrome (MERS-CoV) [12]. In the 2019 Wuhan Outbreak, Chen et. al. used a next-generation RNA-based metagenomic sequencing technique to diagnose human coronaviruses from two cases of pneumonia. Its whole genome length was 29 881 bp [13]. Phylogènetic research reveals that SARS-CoV-2 has a similar characteristic with the bat coronavirus Bt-CoV/4991 bat coronavirus (Gen Bank KP876546, 370 bp rdRp) and 87.9% nucleotide similarity to bat coronavirus strain Bat-SL-CoVZC4-5 and bat-SL-CosV-45, as well as RNRp (RdRp) partial RNAdependent RNA (RdRp) bat coronavirus strain. An evolutionary research based on the genes ORF1a/1b, S and N indicates that SARS-CoV-2 is more likely to be a new corona virus [14]. Based on the results of some genomic research, SARS-CoV-2 infections could be linked to bats slaughters and droppings which can be found in Wuhan seafood market [15]. Many drugs used for the treatment of SARS-Cov-2 are work by the inhibition of protease (Mpro) replication [16,17]. N-acetyl cysteine (NAC) which have been used as an antioxidant [18,19] due to its ability to facilitates the synthesis of glutathione, has been used to decrease the severity and frequency of wheezing, coughing and respiratory attacks [20][21][22], it also used to treat acetaminophen overdose [23,24]. Furthermore, NAC acts as ROS (reactive oxygen species) scavenger [25], therefore it can decreases the inflammation [26].
Also, NAC showed inhibition activity against main protease in viruses, therefore, NAC may improve weakened cellular immunity and avoid the production of certain respiratory viruses, such as HIV and RSV, and has the potential to inhibit SARS-Cov-22 (M pro ) [27][28][29]. The aim of this research was studying the binding of some NAC derivatives with M pro of SARS-CoV-2 complex using docking analysis .

Molecular
docking studies.
In this investigation, Autodock tools docking software was used to understand the interaction of NAC, NACBn, NACEt and NACA with M pro active site. The crystal structures of the protein 6LU7 of COVID-SARS-2 used in this study was obtained from Databank (https://www.rcsb.org/) as PDB format. The selected drug molecules structures (NAC, NACBn, NACEt and NACA which used as ligands) were obtained from drug bank database as PDB formats, To determine the active site of (6LU7) the position of the native ligand on the binding site (Thr26, Tyr54, Phe140, Asn142, Gly143, Ser144, Cys145, His163, His164, Glu166, and His172) was used.

results and Discussion
Because of SARS-COV-2 main protease (M pro ) play important rule in replication the major part of research focus on targeting it's with some drugs. It will be useful to use computational biology and chemistry information to predict the binding abilities of 6LU7-the main protease (M pro ) of the SARS-CoV-2 with drug molecules in order to study the possible interaction with its. The properties of ligands are shown in Table 1 backbone atoms for NAC showed stability. NACBn, however, showed increase in the RMSD value and maintained at 3.5 Å, which is directly similar to the analysis of the charge. For each residue, the RMSF captures the fluctuations from its average position to determine the flexibility of the M pro regions. The parameter RMSF indicates the mobility of the residues. The higher value of RMSF indicates a loosely bonded structure with twists, curves and coils, while the lower value of RMSF indicates a stable secondary structure including alpha-helix and betasheets. We conclude that NACBn does not cause any flexibility as seen from the RMSF outcome and that it is a good complex as opposed to NACBn (Fig. 3).
The hydrogen bonding patterns in both ligand complexes were the same (Fig. 4). Until the last simulation, the NACBn had only two hydrogen bonds. Both ligands are stable and form hydrogen bonds with the protein, based on the hydrogen bond findings. from radius of gyration (Rg) During 50 ns of the process dynamics simulation, the Rg value of the protein in the complex with NACBn was average about 2.32 nm, which presented that the protein retained a stable structure during MDs (Fig. 5). Fig. 6 shows the change of SASA of native and ligands with time.  it appears that evidently NACBn, during their simulations, could have interacted with many atoms of protein residues, and consequently increased their difusibility (Fig. 7). Conclusion. A complex of the best binding configuration of NACBn with protein M pro was run MDs in 50 ns. Combining the molecular docking and MDs, the results showed that NACBn ligand might have the ability to inhibit SARS-CoV-2 replication pathway compared to NAC drug. The Topological Polar Surface Area (TPSA) was calculated for all compounds that haves High PSA value (PSA < 75 Å²) were associated with poor membrane permeability. In the other hand all compounds exhibit computational TPSA values less then (140 Å²) haves good intestinal absorption. However, the derivatives do not have adequate blood-brain barrier penetration, as the TPSA values are more than (60 Å 2 ). According to values of Lipinski's rule of five: all compounds that have Log P value less than 5 and its molecular masses less than 500 Daltons are in good agreement with the given criteria and can be said to possess good oral bioavailability.
Conflict of interest. Authors have completed the Unified Conflicts of Interest form at http://ukrbiochemjournal.org/wp-content/uploads/2018/12/ coi_disclosure.pdf and declare no conflict of interest.