PMID- 34909175
OWN - NLM
STAT- MEDLINE
DCOM- 20211224
LR  - 20220531
IS  - 2046-1402 (Electronic)
IS  - 2046-1402 (Linking)
VI  - 10
DP  - 2021
TI  - Molecular docking and dynamic simulation of conserved B cell epitope of 
      SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach.
LID - Chem Inf Sci-813 [pii]
LID - 10.12688/f1000research.54258.1 [doi]
AB  - Background: An immunoinformatic approach may be useful to investigate the 
      conserved region in the spike glycoprotein of severe acute respiratory syndrome 
      coronavirus 2 (SARS-CoV-2) Indonesia isolates. The aim of this study was to 
      investigate Indonesian SARS-CoV-2 isolates based on B cell epitopes by targeting 
      the conserved regions in the spike glycoprotein to trigger increased 
      multi-variant virus neutralization and memory response for the development of 
      vaccine seed candidates. Methods: SARS-CoV-2 spike glycoprotein gene sequences 
      originating from Indonesia were compared with Wuhan (China), the United Kingdom, 
      South Africa, India, the United States, and Brazil isolates obtained from the 
      NCBI and GISAID databases. The recognition of antigens was carried out directly 
      using B cells through the B cell receptor (BCR). An indirect B cell activation by 
      Cluster of Differentiation (CD)4+ T cells and major histocompatibility complex 
      (MHC)-II was predicted through the binding with human leukocyte antigen (HLA) 
      based on IC (50) value. In addition, vaccine allergenicity and toxicity were 
      investigated. During the molecular complex examination, the 3D peptide structure 
      was investigated and the lowest amount of energy formed when the vaccine 
      candidate peptide bound to BCR and MHC-II was calculated. Results: As a result, 
      the spike glycoprotein sequences of Indonesian SARS-CoV-2 isolates had conserved 
      regions which were very similar to reference countries such as China, the United 
      Kingdom, South Africa, India, the United States, and Brazil. Conclusion: It was 
      predicted that the conserved regions could be identified as the epitope of B and 
      T CD4+ cells that produced the peptides for vaccine candidate with antigenic, 
      non-allergen, and non-toxic properties.
CI  - Copyright: (c) 2021 Rantam FA et al.
FAU - Rantam, Fedik Abdul
AU  - Rantam FA
AUID- ORCID: 0000-0001-8182-1465
AD  - Research Center for Vaccine Technology and Development, Institute of Tropical 
      Disease, Universitas Airlangga, Surabaya, East Java, Indonesia.
AD  - Virology and Immunology Laboratory, Department of Microbiology, Faculty of 
      Veterinary Medicine, Airlangga University, Surabaya, East Java, 60132, Indonesia.
FAU - Kharisma, Viol Dhea
AU  - Kharisma VD
AUID- ORCID: 0000-0001-9060-0429
AD  - Biology Department, Faculty of Mathematic and Natural Sciences, Universitas 
      Brawijaya, Malang, East Java, Indonesia.
FAU - Sumartono, Christrijogo
AU  - Sumartono C
AD  - Anasthesiology and Reanimation Department, Dr. Soetomo Gerneral Hospital and 
      Faculty of Medicine, Universitas Airlangga,, Surabaya, East Java, Indonesia.
FAU - Nugraha, Jusak
AU  - Nugraha J
AUID- ORCID: 0000-0001-6700-9921
AD  - Clinical Pathology Department,, Dr. Soetomo Gerneral Hospital and Faculty of 
      Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia.
FAU - Wijaya, Andi Yasmin
AU  - Wijaya AY
AD  - Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia.
FAU - Susilowati, Helen
AU  - Susilowati H
AD  - Research Center for Vaccine Technology and Development, Institute of Tropical 
      Disease, Universitas Airlangga, Surabaya, East Java, Indonesia.
FAU - Kuncorojakti, Suryo
AU  - Kuncorojakti S
AD  - Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas 
      Airlangga, Surabaya, East Java, Indonesia.
FAU - Nugraha, Alexander Patera
AU  - Nugraha AP
AD  - Orthodontics Department, Universitas Airlangga, Surabaya, East Java, 60132, 
      Indonesia.
LA  - eng
SI  - figshare/10.6084/m9.figshare.15048513.v1
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210816
PL  - England
TA  - F1000Res
JT  - F1000Research
JID - 101594320
RN  - 0 (Epitopes, B-Lymphocyte)
RN  - 0 (Histocompatibility Antigens Class II)
RN  - 0 (Spike Glycoprotein, Coronavirus)
RN  - 0 (spike protein, SARS-CoV-2)
RN  - SARS-CoV-2 variants
SB  - IM
MH  - COVID-19
MH  - Conserved Sequence
MH  - *Epitopes, B-Lymphocyte/immunology
MH  - Histocompatibility Antigens Class II
MH  - Humans
MH  - Indonesia
MH  - Molecular Docking Simulation
MH  - Molecular Dynamics Simulation
MH  - SARS-CoV-2
MH  - Spike Glycoprotein, Coronavirus/*immunology
PMC - PMC8596179
OTO - NOTNLM
OT  - COVID-19
OT  - Immunoinformatic
OT  - Infectious Disease
OT  - SARS-CoV-2
OT  - conserved region.
OT  - spike glycoprotein
COIS- No competing interests were disclosed.
EDAT- 2021/12/16 06:00
MHDA- 2021/12/25 06:00
PMCR- 2021/08/16
CRDT- 2021/12/15 12:29
PHST- 2021/07/28 00:00 [accepted]
PHST- 2021/12/15 12:29 [entrez]
PHST- 2021/12/16 06:00 [pubmed]
PHST- 2021/12/25 06:00 [medline]
PHST- 2021/08/16 00:00 [pmc-release]
AID - Chem Inf Sci-813 [pii]
AID - 10.12688/f1000research.54258.1 [doi]
PST - epublish
SO  - F1000Res. 2021 Aug 16;10:Chem Inf Sci-813. doi: 10.12688/f1000research.54258.1. 
      eCollection 2021.