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(N) Protein from Novel Coronavirus SARS-Cov-2

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(N) Protein from Novel Coronavirus SARS-Cov-2 Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 25 May 2020 doi:10.20944/preprints202005.0413.v1 Characterization of nucleocapsid (N) protein from novel coronavirus SARS-CoV-2 Abhishek Kumar1, 2, * Alisha Parveen3, Narendra Kumar4, Sneha Bairy5, Vibha Kaushik6, Chetan Chandola1, Jyoti Sharma1, 2,, Phulwanti Sharma6, Akhil Agarwal7, Akhilesh Pandey2, 8. 9, Pankaj Goyal6, * and Muniasamy Neerathilingam1, 2, * 1Institute of Bioinformatics, International Technology Park, Bangalore, 560066 India 2Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India 3 Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany; 4Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan - 173 234, Himachal Pradesh, India 5Institute for Stem Cell Science and Regenerative Medicine, GKVK - Post, Bellary Rd, Bengaluru, Karnataka 560065, India 6Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Rajasthan 305817 India 7Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Rajasthan 305817 India 8Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India 9Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States 7Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States *To whom correspondence may be addressed: AK - [email protected]; Tel.: +91 80-2841-6140 PG - [email protected] MN - [email protected]; Tel.: +91 80-2841-6140 © 2020 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 25 May 2020 doi:10.20944/preprints202005.0413.v1 Abstract report this protein has large patches of Severe acute respiratory syndrome novel disordered regions flanking with these coronavirus 2 (SARS-CoV-2) has caused seven motifs. These motifs are hubs of the global pandemic as COVID-19, which epitopes with 67 experimentally verified is the most notorious global public health epitopes from related viruses. We report the crisis in the last 100 years. SARS-CoV-2 presence of three nuclear localization is composed of four structural proteins and signals (NLS1-NLS3 mapped to 36-41, several non-structured proteins. The 256-26, and 363-389 residues, respectively) multi-facet nucleocapsid (N) protein is the and two nuclear export signals (NES1- maJor component of structural proteins of NLS2 from 151-161 and 217-230 residues, CoVs, However, there are no dedicated respectively) in the N protein of SARS- genomic, sequences and structural CoV-2. These deciphered two Q-patches as analyses focusing on potential roles of N Q-patch1 and Q-patch2, mapped in the protein. Hence, there is an urgent regions of 266-306, and 361-418 residues, requirement of a detailed study on N which potentially help in the aggregation of protein of SARS-CoV-2. Herein, we are the viral proteins along with presenting a comprehensive study on N 219LALLLLDR226 patch. Additionally, we protein from SARS-CoV-2. have identified 14 antiviral drugs We have identified seven motifs conserved potentially binding to seven motifs of N- in the three maJor domains namely N- proteins using docking-based drug terminal domain, linker regions and the C- discovery methods. terminal domains. Out of seven motifs, six motifs are conserved across different Keywords: SARS-CoV-2; nucleocapsid members of coronaviridae, while motif4 is (N); genomics; coronavirus; Wuhan; specific for SARS CoVs with potential Pandemic; amyloidogenic properties. Additionally, we Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 25 May 2020 doi:10.20944/preprints202005.0413.v1 that CoV have tendencies to break species 1. Introduction boundaries during infecting humans, they A novel coronavirus (CoV) named as use intermediate hosts such as bats, ant- severe acute respiratory syndrome eaters and camels [1,2]. Hence, it is coronavirus 2 (SARS-CoV-2, initially cautioned that CoV-based infections will called as 2019-nCoV) pushed the entire come back every now and then with our world on a halt with outbreak of exposure to intermediate hosts most coronavirus disease 2019 (COVID-19). probably from a wild animal species [2]. This disease has rapidly become a new Although known that CoV clearly causes emerging human disease and a global infections multiple times and every time a pandemic as SARS-CoV-2 has already new infection comes, we tend to control its infected more than 4,731,458 people across impact by containing spread of the virus by globe and over 316,169 deaths due to lockdown and using other viral drugs. It is COVID-19 as Situation Report–120 of the high time that we focus on CoV using World Health Organization (WHO, an insight out approach focusing on the Webpage long term solutions for the current disease – https://www.who.int/emergencies/diseases COVID19 and also how we can counter any /novel-coronavirus-2019 on 19th May other future outbreak of the CoV. Hence, it 2020). is an urgent requirement that several This suggested that the rate of mortality is computational methods have to come up for 6.7%, which is higher than initial characterization of various components of estimation of about 2%. Several countries CoV genetics and biology. This will be have locked down their cities, states and unravelling future therapeutic targets their international borders, which has led against SARS-CoV-2 and related viruses. almost no international travels and We have an advantage now that using next- ultimately resulted in a massive slowdown generation sequencing methods several in the global economy and businesses. genomes of CoV are available and massive Coronaviruses (CoV) are members of global attempts are made to make more and coronaviridae (NCBI Taxonomy ID: more genomic data to be available soon. 69399) and these are enveloped positive- Recently available genome of SARS-CoV- sense, single-stranded RNA viruses. These 2 is 29.3 kb in size (NCBI Accession ID members of coronaviridae are evolutionary ASM985889v3) harbouring four essential grouped into four genera with Greek structural proteins, including spike (S) number prefixes as alpha (α-CoV), beta (β- glycoprotein, small envelope (E) protein, CoV), gamma (γ-CoV) and delta- matrix (M) protein, and nucleocapsid (N) coronaviruses (δ-CoV). CoVs are known to protein [3]. The nucleocapsid (N) protein of cause infections of the mammalian a coronavirus is a multifunctional protein respiratory and gastrointestinal tracts, but that plays a crucial role in virus assembly the infection mechanism of these viruses is and in its RNA transcription. The N protein not fully understood. The current virus is crucial in the formation of helical SARS-CoV-2 is seventh CoV, which ribonucleoproteins during packaging the caused infections to humans and the other RNA genome, regulating viral RNA four infections by members of β-CoV synthesis during replication, transcription. genera were SARS, Middle East respiratory This protein is also capable of regulating syndrome (MERS), HCoV-OC43 and infected host cells and their cellular HCoV-HKU1, while two α-CoV infections mechanisms. The primary functions of N were reported as HCoV-NL63 and HCoV- protein are binding to the viral RNA 229E. One examining carefully, it is clear genome, and packing them into a long Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 25 May 2020 doi:10.20944/preprints202005.0413.v1 helical nucleocapsid structure or therapeutic targets and epitome inventories. ribonucleoprotein (RNP) complex. The N We have seven motifs with different roles protein possesses highly immunogenic either coronaviridae-specific (motif2) or properties and it is a highly expressed SARS-CoVs-specific (motif4), two protein during infection, capable of glutamine-rich Q-patches and potential inducing protective immune responses roles in generating higher aggregation against SARS-CoV and SARS-CoV-2. propensity in the human cells. We also explored a library of FDA- Herein, we have carried on a approved drugs against seven motifs of N comprehensive characterization of protein for their roles as anti-SARS-CoV-2 nucleocapsid N protein of SARS-CoV-2 drugs and usages in drug repurposing and from sequence, phylogenetic and structural maJority of drugs are HIV perspectives for deciphering potential Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 25 May 2020 doi:10.20944/preprints202005.0413.v1 visualized using either ESPrint3.0 tool [10] 2. Materials and Methods and/or JALVIEW [11]. Homology model 2.1. Scanning nucleocaspid (N) proteins of full length N protein (accession ID - of several coronavirus genomes QHD43423.pdb) was taken from I- TASSER [12]. This protein sequence We detected putative nucleocapsid (N) alignment was constructed using Muscle proteins from different viruses using alignment tool and this protein sequence −10 BLASTP [4] with an E-value < 1e with alignment is visualized along with nucleocapsid (N) protein (Genbank secondary structural elements using Accession ID YP_009724397.2) as the ESPrint3.0 tool [10]. We predicted nuclear query after setting up the local BLAST localization and nuclear export locations database. We performed annotation of these using and NetNES1.1 [13], respectively sequences using OMICSBOX [5] and and these signals are manually curated CELLO2GO [6]. further. We analysed disordered regions
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