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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T6 977-984 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T7 1046-1058 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T8 1106-1122 Body_part denotes epithelial cells http://purl.org/sig/ont/fma/fma66768
T9 1117-1122 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T10 1143-1155 Body_part denotes cell surface http://purl.org/sig/ont/fma/fma67653
T11 1143-1147 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T12 1236-1246 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T13 1309-1316 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T14 2037-2045 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T15 2546-2554 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T16 2902-2910 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T17 3076-3083 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T18 3260-3272 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T19 3282-3289 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 3569-3576 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T21 4343-4350 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T22 4802-4807 Body_part denotes helix http://purl.org/sig/ont/fma/fma60992
T23 4907-4915 Body_part denotes arginine http://purl.org/sig/ont/fma/fma82763
T24 5126-5132 Body_part denotes lysine http://purl.org/sig/ont/fma/fma82758
T25 5172-5178 Body_part denotes valine http://purl.org/sig/ont/fma/fma82766
T26 5331-5338 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T27 5718-5725 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 5883-5890 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T29 6169-6177 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T30 6493-6501 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T31 6549-6557 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T32 6877-6885 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T33 7141-7149 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T34 7168-7173 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T35 7234-7242 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T36 7279-7286 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T37 7647-7655 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T38 8375-8382 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T39 8542-8550 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 4802-4807 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T2 7168-7173 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p8111s23 4986-4995 NegReg denotes abolished
p8111s25 5000-5006 MPA denotes strong
p8111s26 5007-5025 MPA denotes polar interactions
p8111s33 5046-5054 NegReg denotes decrease
p8111s36 5062-5086 Interaction denotes binding affinity between
p8112s39 5276-5291 MPA denotes binding ability

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T10 223-236 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T11 479-498 Disease denotes 2019-nCoV infection http://purl.obolibrary.org/obo/MONDO_0100096
T12 489-498 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T13 685-718 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T14 771-775 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T15 887-891 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T16 905-913 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 992-1000 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 1442-1450 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 1523-1531 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 1807-1815 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 1922-1930 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 1979-1987 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 2179-2187 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 2248-2250 Disease denotes VL http://purl.obolibrary.org/obo/MONDO_0024555
T25 2386-2388 Disease denotes VL http://purl.obolibrary.org/obo/MONDO_0024555
T26 2424-2432 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 2682-2690 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 2718-2726 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 2816-2824 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 3035-3043 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 3507-3515 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 3613-3621 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 3705-3713 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 3783-3791 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 3800-3808 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 3890-3898 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 4528-4536 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 4811-4819 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 4925-4933 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 5188-5196 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 5396-5404 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 5703-5711 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 5965-5973 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 6859-6867 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 7192-7196 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T46 7799-7807 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 7955-7963 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 8232-8240 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T49 8335-8343 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T50 8600-8608 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T51 8795-8803 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T52 9066-9086 Disease denotes 2019-nCoV infections http://purl.obolibrary.org/obo/MONDO_0100096
T53 9151-9159 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T11 15-16 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T12 162-165 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T13 178-179 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T14 217-222 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T15 270-273 http://purl.obolibrary.org/obo/CLO_0054061 denotes 132
T16 607-608 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T17 672-675 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T18 679-684 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T19 767-770 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T20 812-813 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 838-839 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 1023-1024 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 1088-1093 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T24 1106-1116 http://purl.obolibrary.org/obo/CL_0000066 denotes epithelial
T25 1117-1122 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T26 1143-1147 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T27 1556-1561 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T28 1565-1566 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 1837-1838 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T30 2022-2023 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 2217-2218 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 2563-2565 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T33 3216-3217 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 3364-3370 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T35 3456-3457 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T36 4213-4214 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 4215-4218 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T38 4449-4454 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T39 4831-4832 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 4859-4860 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 5044-5045 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 5124-5125 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 5374-5375 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 5467-5472 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T45 5634-5639 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T46 5731-5736 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T47 6065-6075 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T48 6132-6133 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 6152-6157 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T50 6514-6515 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 7001-7002 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 7012-7015 http://purl.obolibrary.org/obo/CLO_0009946 denotes kon
T53 7030-7034 http://purl.obolibrary.org/obo/CLO_0007875 denotes Ms−1
T54 7030-7034 http://purl.obolibrary.org/obo/CLO_0050048 denotes Ms−1
T55 7030-7034 http://purl.obolibrary.org/obo/CLO_0052410 denotes Ms−1
T56 7070-7073 http://purl.obolibrary.org/obo/CLO_0050050 denotes s−1
T57 7106-7110 http://purl.obolibrary.org/obo/CLO_0001692 denotes a KD
T58 7168-7173 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T59 7168-7173 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T60 7177-7178 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 7387-7392 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T62 7460-7468 http://purl.obolibrary.org/obo/CLO_0007225 denotes labelled
T63 7521-7526 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T64 7577-7581 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T65 8036-8037 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 8138-8139 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 8631-8638 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T68 8642-8643 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 8807-8808 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 8909-8912 http://purl.obolibrary.org/obo/CLO_0051582 denotes has

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T7 451-460 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587
T8 794-796 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T9 977-984 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T10 1005-1007 Chemical denotes SL http://purl.obolibrary.org/obo/CHEBI_74815
T11 1046-1058 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T12 1165-1176 Chemical denotes angiotensin http://purl.obolibrary.org/obo/CHEBI_48433
T13 1236-1246 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T14 1236-1241 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T15 1242-1246 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T16 1309-1316 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T17 2219-2223 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T19 2248-2250 Chemical denotes VL http://purl.obolibrary.org/obo/CHEBI_75013
T20 2386-2388 Chemical denotes VL http://purl.obolibrary.org/obo/CHEBI_75013
T21 2647-2651 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T23 2710-2714 Chemical denotes R162 http://purl.obolibrary.org/obo/CHEBI_85885
T24 3076-3083 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T25 3260-3272 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T26 3282-3289 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T27 3356-3360 Chemical denotes MEGA http://purl.obolibrary.org/obo/CHEBI_6617
T28 3569-3576 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T29 4343-4350 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T30 4738-4746 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T31 4833-4837 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T33 4861-4869 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T34 4907-4915 Chemical denotes arginine http://purl.obolibrary.org/obo/CHEBI_16467|http://purl.obolibrary.org/obo/CHEBI_29016|http://purl.obolibrary.org/obo/CHEBI_32696
T37 4942-4952 Chemical denotes asparagine http://purl.obolibrary.org/obo/CHEBI_22653
T38 5126-5132 Chemical denotes lysine http://purl.obolibrary.org/obo/CHEBI_18019|http://purl.obolibrary.org/obo/CHEBI_25094
T40 5172-5178 Chemical denotes valine http://purl.obolibrary.org/obo/CHEBI_27266
T41 5224-5228 Chemical denotes salt http://purl.obolibrary.org/obo/CHEBI_24866|http://purl.obolibrary.org/obo/CHEBI_26710
T43 5331-5338 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T44 5608-5610 Chemical denotes KD http://purl.obolibrary.org/obo/CHEBI_73601
T45 5718-5725 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T46 5883-5890 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T47 7108-7110 Chemical denotes KD http://purl.obolibrary.org/obo/CHEBI_73601
T48 7279-7286 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T49 7535-7543 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T50 7834-7841 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T51 8375-8382 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T52 8754-8761 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004
T53 9248-9257 Chemical denotes antiviral http://purl.obolibrary.org/obo/CHEBI_22587

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T14 0-128 Sentence denotes Very recently, a novel coronavirus which was temporarily named “2019 novel coronavirus (2019-nCoV)” emerged in Wuhan, China [1].
T15 129-406 Sentence denotes As of 1 February 2020, 2019-nCoV has resulted in a total of 11,821 laboratory-confirmed human infections in China, including 259 deaths, and 132 exported cases in 23 countries outside of China (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports).
T16 407-499 Sentence denotes Currently, there is no vaccine or effective antiviral treatment against 2019-nCoV infection.
T17 500-556 Sentence denotes Based on the phylogenetic analysis (GISAID accession no.
T18 557-816 Sentence denotes EPI_ISL_402124) [2], 2019-nCoV belongs to lineage B betacoronavirus and shares high sequence identity with that of bat or human severe acute respiratory syndrome coronavirus-related coronavirus (SARSr-CoV) and bat SARS-like coronavirus (SL-CoV) (Figure 1(a)).
T19 817-942 Sentence denotes In previous studies, a number of potent monoclonal antibodies against SARS coronavirus (SARS-CoV) have been identified [3–7].
T20 943-1208 Sentence denotes These antibodies target the spike protein (S) of SARS-CoV and SL-CoVs, which is a type I transmembrane glycoprotein and mediates the entrance to human respiratory epithelial cells by interacting with cell surface receptor angiotensin-converting enzyme 2 (ACE2) [8].
T21 1209-1372 Sentence denotes More specifically, the 193 amino acid length (N318-V510) receptor binding domain (RBD) within the S protein is the critical target for neutralizing antibodies [9].
T22 1373-1591 Sentence denotes Some of the antibodies recognize different epitopes on RBD; e.g. the SARS-CoV neutralizing antibodies CR3014 and CR3022 bound noncompetitively to the SARS-CoV RBD and neutralized the virus in a synergistic fashion [5].
T23 1592-1841 Sentence denotes We predicted the conformation of 2019-nCoV RBD as well as its complex structures with several neutralizing antibodies, and found that the modelling results support the interactions between 2019-nCoV RBD and certain SARS-CoV antibodies (Figure 1(b)).
T24 1842-1945 Sentence denotes This could be due to the relatively high identity (73%) of RBD in 2019-nCoV and SARS-CoV (Figure 1(c)).
T25 1946-2158 Sentence denotes For instance, residues in RBD of SARS-CoV that make polar interactions with a neutralizing antibody m396 as indicated by the complex crystal structure [10] are invariably conserved in 2019-nCoV RBD (Figure 1(d)).
T26 2159-2251 Sentence denotes In the structure of SARS-CoV-RBD-m396, R395 in RBD formed a salt bridge with D95 of m396-VL.
T27 2252-2390 Sentence denotes Concordantly, the electrostatic interaction was also observed in the model of 2019-nCoV-RBD-m396, forming by R408 (RBD) and D95 (m396-VL).
T28 2391-2507 Sentence denotes This analysis suggests that some SARS-CoV-specific monoclonal antibodies may be effective in neutralizing 2019-nCoV.
T29 2508-2749 Sentence denotes In contrast, the interactions between antibody F26G19 [11] or 80R [12] and the RBD in 2019-nCoV decreased significantly due to the lack of salt bridges formed by R426-D56 in SARS-CoV-RBD-F26G19 or D480-R162 in SARS-CoV-RBD-80R, respectively.
T30 2750-2953 Sentence denotes Furthermore, while most of the 80R-binding residues on the RBD of SARS-CoV are not conserved on RBD of 2019-nCoV (Figure 1(c)), it is unlikely that the antibody 80R could effectively recognize 2019-nCoV.
T31 2954-3204 Sentence denotes Therefore, it is urgent to experimentally determine the cross-reactivity of anti-SARS-CoV antibodies with 2019-nCoV spike protein, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV.
T32 3205-3306 Sentence denotes Figure 1. (a) Phylogenetic analysis of 2019-nCoV spike glycoprotein from its protein BLAST sequences.
T33 3307-4175 Sentence denotes The neighbour-joining tree was constructed using MEGA X, tested by bootstrap method of 2000 replicates, and edited by the online tool of iTOL (v5). (b) The simulated model of 2019-nCoV RBD binding to SARS-CoV-RBD-specific antibodies (m396, 80R, and F26G19). (c) Protein sequence alignment of 2019-nCoV and SARS-CoV RBD, showing the predominant residues that contribute to interactions with ACE2 or SARS-CoV-specific antibodies. (d) The comparison of the complex structures of SARS-CoV-RBD and SARS-CoV-RBD-specific antibodies (shown in the first row) and models of 2019-nCoV-RBD and SARS-CoV-RBD-specific antibodies (shown in the second row). (e) Binding of monoclonal antibodies to 2019-nCoV RBD determined by ELISA. (f) Binding profiles of 2019-nCoV RBD to ACE2 and antibodies, and (g) competition of CR3022 and ACE2 with 2019-nCoV RBD measured by BLI in OctetRED96.
T34 4176-4281 Sentence denotes Binding kinetics was evaluated using a 1:1 Langmuir binding model by ForteBio Data Analysis 7.0 software.
T35 4282-4351 Sentence denotes In this study, we first expressed and purified 2019-nCoV RBD protein.
T36 4352-4460 Sentence denotes We also predicted the conformations of 2019-nCoV RBD and its complex with the putative receptor, human ACE2.
T37 4461-4634 Sentence denotes Comparison of the interaction between the complex of ACE2 [13] and SARS-CoV RBD and homology model of ACE2 and 2019-nCoV RBD revealed similar binding modes (data not shown).
T38 4635-4772 Sentence denotes In both complexes, β5–β6 loop and β6–β7 loop form extensive contact, including at least seven pairs of hydrogen bonds, with the receptor.
T39 4773-4893 Sentence denotes Notably, R426 on the forth α helix in SARS-CoV RBD builds a salt bridge with E329 and a hydrogen bond with Q325 on ACE2.
T40 4894-5108 Sentence denotes However, the arginine (R426 in SARS-CoV RBD) to asparagine (N439) mutation in 2019-nCoV RBD abolished the strong polar interactions, which may induce a decrease in the binding affinity between RBD and the receptor.
T41 5109-5292 Sentence denotes Interestingly, a lysine (K417 in 2019-nCoV RBD) replacement of valine (V404 in SARS-CoV RBD) on β6 formed an extra salt bridge with D30 on ACE2, which may recover the binding ability.
T42 5293-5414 Sentence denotes These data indicate that the RBD in S protein of 2019-nCoV may bind to ACE2 with a similar affinity as SARS-CoV RBD does.
T43 5415-5582 Sentence denotes Indeed, we measured the binding of 2019-nCoV RBD to human ACE2 by the biolayer interferometry binding (BLI) assay, and found that 2019-nCoV RBD bound potently to ACE2.
T44 5583-5755 Sentence denotes The calculated affinity (KD) of 2019-nCoV RBD with human ACE2 was 15.2 nM (Figure 1(f)), which is comparable to that of SARS-CoV spike protein with human ACE2 (15 nM) [14].
T45 5756-5909 Sentence denotes These results indicate that ACE2 could be the potential receptor for the new coronavirus, and that the expressed 2019-nCoV RBD protein is functional [2].
T46 5910-6292 Sentence denotes Next, we expressed and purified several representative SARS-CoV-specific antibodies which have been reported to target RBD and possess potent neutralizing activities, including m396 [3], CR3014 [4], CR3022 [5], as well as a MERS-CoV-specific human monoclonal antibody m336 developed by our laboratory [15], and measured their binding ability to 2019-nCoV RBD by ELISA (Figure 1(e)).
T47 6293-6392 Sentence denotes Surprisingly, we found that most of these antibodies did not show evident binding to 2019-nCoV RBD.
T48 6393-6468 Sentence denotes To confirm this result, we further measured the binding kinetics using BLI.
T49 6469-6533 Sentence denotes An irrelevant anti-CD40 antibody was used as a negative control.
T50 6534-6695 Sentence denotes Similarly, the antibody m396, which was predicted to bind 2019-nCoV RBD (Figure 1(d)), only showed slight binding at the highest measured concentration (2.0 µM).
T51 6696-6845 Sentence denotes Further studies are needed to solve the high-resolution structure of 2019-nCoV RBD and understand why it could not be recognized by these antibodies.
T52 6846-6988 Sentence denotes Notably, one SARS-CoV-specific antibody, CR3022, was found to bind potently with 2019-nCoV RBD as determined by ELISA and BLI (Figure 1(e,f)).
T53 6989-7135 Sentence denotes It followed a fast-on (kon of 1.84 × 105 Ms−1) and slow-off (koff of 1.16 × 10−3 s−1) binding kinetics, resulting in a KD of 6.3 nM (Figure 1(f)).
T54 7136-7291 Sentence denotes This antibody was isolated from blood of a convalescent SARS patient and did not compete with the antibody CR3014 for binding to recombinant S protein [5].
T55 7292-7431 Sentence denotes To further elucidate the binding epitopes of CR3022, we measured the competition of CR3022 and human ACE2 for the binding to 2019-nCoV RBD.
T56 7432-7617 Sentence denotes The streptavidin biosensors labelled with biotinylated 2019-nCoV RBD were saturated with human ACE2 in solution, followed by the addition of the test antibodies in the presence of ACE2.
T57 7618-7735 Sentence denotes As shown in Figure 1(g), the antibody CR3022 did not show any competition with ACE2 for the binding to 2019-nCoV RBD.
T58 7736-7908 Sentence denotes These results suggest that CR3022, distinct from the other two SARS-CoV antibodies, recognizes an epitope that does not overlap with the ACE2 binding site of 2019-nCoV RBD.
T59 7909-8005 Sentence denotes The RBD of 2019-nCoV differs largely from the SARS-CoV at the C-terminus residues (Figure 1(c)).
T60 8006-8207 Sentence denotes Our results implied that such a difference did not result in drastic changes in the capability to engage the ACE2 receptor, but had a critical impact on the cross-reactivity of neutralizing antibodies.
T61 8208-8501 Sentence denotes Some of the most potent SARS-CoV-specific neutralizing antibodies (e.g. m396, CR3014) that target the receptor binding site of SARS-CoV failed to bind 2019-nCoV spike protein, indicating that it is necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD.
T62 8502-8736 Sentence denotes Interestingly, it was reported that the antibody CR3022 completely neutralized both the wild-type SARS-CoV and the CR3014 escape viruses at a concentration of 23.5 μg/ml, and that no escape variants could be generated with CR3022 [5].
T63 8737-8874 Sentence denotes Furthermore, the mixture of CR3022 and CR3014 neutralized SARS-CoV in a synergistic fashion by recognizing different epitopes on RBD [5].
T64 8875-9087 Sentence denotes These results suggest that CR3022 has the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infections.
T65 9088-9284 Sentence denotes We expect more cross-reactive antibodies against 2019-nCoV and SARS-CoV or other coronaviruses to be identified soon, facilitating the development of effective antiviral therapeutics and vaccines.
T66 9286-9308 Sentence denotes Supplementary Material
T67 9309-9330 Sentence denotes Supplemental Material

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
71 17-34 Species denotes novel coronavirus Tax:2697049
72 64-86 Species denotes 2019 novel coronavirus Tax:2697049
73 88-97 Species denotes 2019-nCoV Tax:2697049
74 152-161 Species denotes 2019-nCoV Tax:2697049
75 217-222 Species denotes human Tax:9606
76 223-233 Disease denotes infections MESH:D007239
77 258-264 Disease denotes deaths MESH:D003643
78 370-386 Disease denotes coronavirus-2019 MESH:C000657245
79 479-498 Disease denotes 2019-nCoV infection MESH:C000657245
97 3697-3701 Gene denotes ACE2 Gene:59272
98 4066-4070 Gene denotes ACE2 Gene:59272
99 4121-4125 Gene denotes ACE2 Gene:59272
100 3244-3253 Species denotes 2019-nCoV Tax:2697049
101 3482-3491 Species denotes 2019-nCoV Tax:2697049
102 3507-3515 Species denotes SARS-CoV Tax:694009
103 3599-3608 Species denotes 2019-nCoV Tax:2697049
104 3613-3621 Species denotes SARS-CoV Tax:694009
105 3783-3791 Species denotes SARS-CoV Tax:694009
106 3800-3808 Species denotes SARS-CoV Tax:694009
107 3872-3881 Species denotes 2019-nCoV Tax:2697049
108 3890-3898 Species denotes SARS-CoV Tax:694009
109 3990-3999 Species denotes 2019-nCoV Tax:2697049
110 4049-4058 Species denotes 2019-nCoV Tax:2697049
111 4131-4140 Species denotes 2019-nCoV Tax:2697049
112 3705-3713 Species denotes SARS-CoV Tax:694009
113 4110-4116 Chemical denotes CR3022
153 1165-1196 Gene denotes angiotensin-converting enzyme 2 Gene:59272
154 1198-1202 Gene denotes ACE2 Gene:59272
155 578-587 Species denotes 2019-nCoV Tax:2697049
156 609-624 Species denotes betacoronavirus Tax:694002
157 679-684 Species denotes human Tax:9606
158 685-730 Species denotes severe acute respiratory syndrome coronavirus Tax:694009
159 739-750 Species denotes coronavirus Tax:11118
160 752-761 Species denotes SARSr-CoV Tax:694009
161 767-792 Species denotes bat SARS-like coronavirus Tax:1508227
162 797-800 Species denotes CoV Tax:11118
163 887-903 Species denotes SARS coronavirus Tax:694009
164 905-913 Species denotes SARS-CoV Tax:694009
165 992-1000 Species denotes SARS-CoV Tax:694009
166 1008-1012 Species denotes CoVs Tax:11118
167 1088-1093 Species denotes human Tax:9606
168 1523-1531 Species denotes SARS-CoV Tax:694009
169 1625-1634 Species denotes 2019-nCoV Tax:2697049
170 1781-1790 Species denotes 2019-nCoV Tax:2697049
171 1908-1917 Species denotes 2019-nCoV Tax:2697049
172 1922-1930 Species denotes SARS-CoV Tax:694009
173 1979-1987 Species denotes SARS-CoV Tax:694009
174 2130-2139 Species denotes 2019-nCoV Tax:2697049
175 2179-2187 Species denotes SARS-CoV Tax:694009
176 2330-2339 Species denotes 2019-nCoV Tax:2697049
177 2497-2506 Species denotes 2019-nCoV Tax:2697049
178 2594-2603 Species denotes 2019-nCoV Tax:2697049
179 2682-2690 Species denotes SARS-CoV Tax:694009
180 2718-2726 Species denotes SARS-CoV Tax:694009
181 2816-2824 Species denotes SARS-CoV Tax:694009
182 2853-2862 Species denotes 2019-nCoV Tax:2697049
183 2943-2952 Species denotes 2019-nCoV Tax:2697049
184 3060-3069 Species denotes 2019-nCoV Tax:2697049
185 3194-3203 Species denotes 2019-nCoV Tax:2697049
186 1442-1450 Species denotes SARS-CoV Tax:694009
187 1807-1815 Species denotes SARS-CoV Tax:694009
188 2424-2432 Species denotes SARS-CoV Tax:694009
189 3035-3043 Species denotes SARS-CoV Tax:694009
190 1475-1481 Chemical denotes CR3014
191 1486-1492 Chemical denotes CR3022
234 4455-4459 Gene denotes ACE2 Gene:59272
235 4514-4518 Gene denotes ACE2 Gene:59272
236 4563-4567 Gene denotes ACE2 Gene:59272
237 4888-4892 Gene denotes ACE2 Gene:59272
238 5248-5252 Gene denotes ACE2 Gene:59272
239 5364-5368 Gene denotes ACE2 Gene:59272
240 5473-5477 Gene denotes ACE2 Gene:59272
241 5577-5581 Gene denotes ACE2 Gene:59272
242 5640-5644 Gene denotes ACE2 Gene:59272
243 5737-5741 Gene denotes ACE2 Gene:59272
244 5784-5788 Gene denotes ACE2 Gene:59272
245 4329-4338 Species denotes 2019-nCoV Tax:2697049
246 4391-4400 Species denotes 2019-nCoV Tax:2697049
247 4449-4454 Species denotes human Tax:9606
248 4528-4536 Species denotes SARS-CoV Tax:694009
249 4572-4581 Species denotes 2019-nCoV Tax:2697049
250 4811-4819 Species denotes SARS-CoV Tax:694009
251 4925-4933 Species denotes SARS-CoV Tax:694009
252 4972-4981 Species denotes 2019-nCoV Tax:2697049
253 5142-5151 Species denotes 2019-nCoV Tax:2697049
254 5188-5196 Species denotes SARS-CoV Tax:694009
255 5342-5351 Species denotes 2019-nCoV Tax:2697049
256 5396-5404 Species denotes SARS-CoV Tax:694009
257 5450-5459 Species denotes 2019-nCoV Tax:2697049
258 5467-5472 Species denotes human Tax:9606
259 5545-5554 Species denotes 2019-nCoV Tax:2697049
260 5615-5624 Species denotes 2019-nCoV Tax:2697049
261 5634-5639 Species denotes human Tax:9606
262 5703-5711 Species denotes SARS-CoV Tax:694009
263 5731-5736 Species denotes human Tax:9606
264 5829-5844 Species denotes new coronavirus Tax:2697049
265 5869-5878 Species denotes 2019-nCoV Tax:2697049
266 4738-4746 Chemical denotes hydrogen MESH:D006859
267 4850-4854 Chemical denotes E329
268 4861-4869 Chemical denotes hydrogen MESH:D006859
269 4880-4884 Chemical denotes Q325
270 4907-4915 Chemical denotes arginine MESH:D001120
271 4942-4952 Chemical denotes asparagine MESH:D001216
272 5126-5132 Chemical denotes lysine MESH:D008239
273 5134-5138 Chemical denotes K417
274 5172-5178 Chemical denotes valine MESH:D014633
275 5241-5244 Chemical denotes D30 MESH:C005496
286 6488-6492 Gene denotes CD40 Gene:958
287 6134-6142 Species denotes MERS-CoV Tax:1335626
288 6255-6264 Species denotes 2019-nCoV Tax:2697049
289 6378-6387 Species denotes 2019-nCoV Tax:2697049
290 6592-6601 Species denotes 2019-nCoV Tax:2697049
291 6765-6774 Species denotes 2019-nCoV Tax:2697049
292 5965-5973 Species denotes SARS-CoV Tax:694009
293 6152-6157 Species denotes human Tax:9606
294 6097-6103 Chemical denotes CR3014
295 6109-6115 Chemical denotes CR3022
317 7393-7397 Gene denotes ACE2 Gene:59272
318 7527-7531 Gene denotes ACE2 Gene:59272
319 7612-7616 Gene denotes ACE2 Gene:59272
320 7697-7701 Gene denotes ACE2 Gene:59272
321 7873-7877 Gene denotes ACE2 Gene:59272
322 6927-6936 Species denotes 2019-nCoV Tax:2697049
323 7197-7204 Species denotes patient Tax:9606
324 7387-7392 Species denotes human Tax:9606
325 7417-7426 Species denotes 2019-nCoV Tax:2697049
326 7487-7496 Species denotes 2019-nCoV Tax:2697049
327 7521-7526 Species denotes human Tax:9606
328 7721-7730 Species denotes 2019-nCoV Tax:2697049
329 7894-7903 Species denotes 2019-nCoV Tax:2697049
330 6859-6867 Species denotes SARS-CoV Tax:694009
331 7799-7807 Species denotes SARS-CoV Tax:694009
332 6887-6893 Chemical denotes CR3022
333 7243-7249 Chemical denotes CR3014
334 7337-7343 Chemical denotes CR3022
335 7376-7382 Chemical denotes CR3022
336 7656-7662 Chemical denotes CR3022
337 7763-7769 Chemical denotes CR3022
357 8115-8119 Gene denotes ACE2 Gene:59272
358 7920-7929 Species denotes 2019-nCoV Tax:2697049
359 7955-7963 Species denotes SARS-CoV Tax:694009
360 8232-8240 Species denotes SARS-CoV Tax:694009
361 8335-8343 Species denotes SARS-CoV Tax:694009
362 8359-8368 Species denotes 2019-nCoV Tax:2697049
363 8487-8496 Species denotes 2019-nCoV Tax:2697049
364 8600-8608 Species denotes SARS-CoV Tax:694009
365 8795-8803 Species denotes SARS-CoV Tax:694009
366 9137-9146 Species denotes 2019-nCoV Tax:2697049
367 9151-9159 Species denotes SARS-CoV Tax:694009
368 9169-9182 Species denotes coronaviruses Tax:11118
369 8551-8557 Chemical denotes CR3022
370 8617-8623 Chemical denotes CR3014
371 8725-8731 Chemical denotes CR3022
372 8765-8771 Chemical denotes CR3022
373 8776-8782 Chemical denotes CR3014
374 8902-8908 Chemical denotes CR3022
375 9066-9086 Disease denotes 2019-nCoV infections MESH:C000657245