key: cord-336394-1xf2sxtv authors: Li, Yu; Zhang, Ziding; Yang, Li; Lian, Xianyi; Xie, Yan; Li, Shen; Xin, Shuyu; Cao, Pengfei; Lu, Jianhong title: The MERS-CoV receptor DPP4 as a candidate binding target of the SARS-CoV-2 spike date: 2020-05-13 journal: iScience DOI: 10.1016/j.isci.2020.101160 sha: doc_id: 336394 cord_uid: 1xf2sxtv SUMMARY The ongoing outbreak of the novel coronavirus pneumonia COVID-19 has caused great number of cases and deaths, but our understanding about the pathogen SARS-CoV-2 remains largely unclear. The attachment of the virus with the cell-surface receptor and a co-factor is the first step for the infection. Here, bioinformatics approaches combining human-virus protein interaction prediction and protein docking based on crystal structures have revealed the high affinity between human dipeptidyl peptidase 4 (DPP4) and the spike (S) receptor-binding domain of SARS-CoV-2. Intriguingly, the crucial binding residues of DPP4 are identical to those as bound to the MERS-CoV-S. Moreover, E484 insertion and adjacent substitutions should be most essential for this DPP4-binding ability acquirement of SARS-CoV-2-S compared with SARS-CoV-S. This potential utilization of DPP4 as a binding target for SARS-CoV-2 may offer novel insight into the viral pathogenesis, and help the surveillance and therapeutics strategy for meeting the challenge of COVID-19. (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports). 43 As an emerging disease caused by the severe acute respiratory syndrome coronavirus 44 2 (SARS-CoV-2, previously named 2019-nCoV), COVID-19 has since become a 45 global concern with the very-high level of risk. The pathogen SARS-CoV-2 has been 46 shown to be a member of betacoronaviruses closely related to the SARS-CoV and the 47 strain RaTG13 of bat origin (Zhou et al., 2020) . 48 The coronaviruses are enveloped ranking among the dangerous zoonotically emerging (Table 1 ). It is known that 121 ACE2 has been proposed to be a receptor of SARS-CoV-2. Since DPP4 obtained the 122 highest integration score (Table 1) , and it is also associated with a betacoronavirus by 123 acting as the receptor of MERS-CoV, we focused on it next. By employing protein docking strategy, we investigated the potential interaction 144 mode between SARS-CoV-2-S RBD and DPP4. The atomic interaction details of the 145 binding interface showed that almost all of the contacting residues of DPP4 with 146 SARS-CoV-2-S RBD were consistent with those for binding with MERS-CoV-S 147 RBD (Table S1 ) (Song et al., 2014) . These residues include: DPP4 residue K267 with 148 Figure 1B and Table S1 ). In addition, DPP4 residue L294 and I295 can contribute 151 Van der Waals' forces to the binding (Table S1) The analysis of key residues for DPP4-binding ability acquirement of 171 According to the above results ( Figure 1A substitutions existed at the sites equivalent to E484 and adjacent residues of 186 SARS-CoV-2, and there were no mutations at the rest three key residues ( Figure S1) . 187 In addition, since the pangolin has been suspected as a zoonotic host of SARS-CoV-2, 188 we compared the sequences of human and pangolin DPP4 ( Figure 3C ). The result 189 showed that they shared all key residues ready to bind to both SARS-CoV-2 and MERS-CoV-S could bind to DPP4, sharing the identical key binding residues of 219 DPP4 at the interfaces (Figure 1) . The results also suggested that the insertion and 220 substitutions at E484 and adjacent residues be essential for the entirely different 221 ability in binding to DPP4 between SARS-CoV-2 and SARS-CoV spikes, for adjacent 222 residues may also contribute to the structure change. It seems that the binding of 223 SARS-CoV-2-S and DPP4 is unique. Whereas, these kinds of mutations can naturally 224 occur as in the bat strain RaTG13 (Figure S1 ), though the residues may be different. 225 The only animal-origin betacoronavirus that possesses this potential binding ability 226 currently is one isolated from pangolins, containing these identical key residues in the 227 spike RBD sequences (Lam et al., 2020) . In addition, the models evaluated the 228 binding potential, interface residues and structures that were consistent with those 229 Comparison of the key residues between human and pangolin DPP4 protein 471 489 Figure S1 . The sequence comparison between SARS-CoV-2-S RBD and that of bat 490 RaTG13 strain, Related to Figure 3 . 491 Table S1 . The key contact residues at the SARS-CoV-2-S RBD/DPP4 and 492 Regulation and roles of CD26/DPPIV in hematopoiesis and diseases Carcinoembryonic antigen-related cell 326 adhesion molecule 5 is an important surface attachment factor that facilitates entry of 327 middle east respiratory syndrome coronavirus Dysregulation of DPP4 is associated with the AMPK/JAK2/STAT3 pathway 331 in adipocytes under insulin resistance status and liraglutide intervention Middle east respiratory syndrome 336 coronavirus and bat coronavirus HKU9 both can utilize GRP78 for attachment onto 337 host cells Origin and evolution of pathogenic coronaviruses The tetraspanin CD9 facilitates MERS-coronavirus entry by scaffolding host 344 cell receptors and proteases The MM/PBSA and MM/GBSA methods to 347 estimate ligand-binding affinities The sequence of human ACE2 is suboptimal for binding the S 350 spike protein of SARS coronavirus 2 SARS-CoV-2 cell 355 entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease 356 inhibitor Identifying SARS-CoV-2 related coronaviruses in 360 Malayan pangolins Crystal structure of the 2019-nCoV spike 364 receptor-binding domain bound with the ACE2 receptor Functional assessment of cell entry and 368 receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses ff14SB: Improving the accuracy of protein side chain and 373 backbone parameters from ff99SB MMPBSA.py: An efficient program for end-state free energy calculations Settle: An analytical version of the SHAKE 380 and RATTLE algorithm for rigid water models Comparative pathogenesis of COVID-19, MERS and SARS in a non-human primate model An overview of the Amber 388 biomolecular simulation package Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis 393 interactomes Dipeptidyl peptidase 4 396 inhibitors and their potential immune modulatory functions Identification of residues on human receptor DPP4 critical for MERS-CoV binding 401 and entry From SARS to MERS, thrusting coronaviruses into the spotlight. 405 Viruses Ewald based approach to fixed and induced dipolar interactions Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. 413 Cell Structure of MERS-CoV spike receptor-binding domain 417 complexed with human receptor DPP4 Viral invasion and type I interferon response characterize the 421 immunophenotypes during Covid-19 infection STRING: Known and predicted 425 protein-protein associations, integrated and transferred across organisms. Nucleic 426 Acids Res Prediction of 429 human-virus protein-protein interactions through a sequence embedding-based 430 machine learning method Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak Stringent homology-based prediction of H. sapiens-M. 438 tuberculosis H37Rv protein-protein interactions SARS-CoV-2 spike receptor-binding domain has a potentially high affinity with DPP4 SARS-CoV-2-S/DPP4 binding shares key DPP4 residues with that of MERS-CoV-S/DPP4 E484 and adjacent mutations are critical for the DPP4-binding ability of SARS-CoV-2-S