PMID- 34960205
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20231108
IS  - 2076-393X (Print)
IS  - 2076-393X (Electronic)
IS  - 2076-393X (Linking)
VI  - 9
IP  - 12
DP  - 2021 Dec 9
TI  - Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify 
      Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for 
      Indonesia and the World Population.
LID - 10.3390/vaccines9121459 [doi]
LID - 1459
AB  - SARS-CoV-2 and its variants caused the COVID-19 pandemic. Vaccines that target 
      conserved regions of SARS-CoV-2 and stimulate protective T-cell responses are 
      important for reducing symptoms and limiting the infection. Seven cytotoxic (CTL) 
      and five helper T-cells (HTL) epitopes from ORF1ab were identified using 
      NetCTLpan and NetMHCIIpan algorithms, respectively. These epitopes were generated 
      from ORF1ab regions that are evolutionary stable as reflected by zero Shannon's 
      entropy and are presented by 56 human leukocyte antigen (HLA) Class I and 22 HLA 
      Class II, ensuring good coverage for the Indonesian and world population. Having 
      fulfilled other criteria such as immunogenicity, IFNgamma inducing ability, and 
      non-homology to human and microbiome peptides, the epitopes were assembled into a 
      vaccine construct (VC) together with beta-defensin as adjuvant and appropriate 
      linkers. The VC was shown to have good physicochemical characteristics and 
      capability of inducing CTL as well as HTL responses, which stem from the 
      engagement of the vaccine with toll-like receptor 4 (TLR4) as revealed by docking 
      simulations. The most promiscuous peptide (899)WSMATYYLF(907) was shown via 
      docking simulation to interact well with HLA-A*24:07, the most predominant allele 
      in Indonesia. The data presented here will contribute to the in vitro study of 
      T-cell epitope mapping and vaccine design in Indonesia.
FAU - Gustiananda, Marsia
AU  - Gustiananda M
AD  - Department of Biomedicine, School of Life Sciences, Indonesia International 
      Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia.
FAU - Sulistyo, Bobby Prabowo
AU  - Sulistyo BP
AUID- ORCID: 0000-0002-5203-4822
AD  - Department of Biomedicine, School of Life Sciences, Indonesia International 
      Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia.
FAU - Agustriawan, David
AU  - Agustriawan D
AUID- ORCID: 0000-0003-1185-1145
AD  - Department of Bioinformatics, School of Life Sciences, Indonesia International 
      Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia.
FAU - Andarini, Sita
AU  - Andarini S
AD  - Department of Pulmonology and Respiratory Medicine, Faculty of Medicine 
      University of Indonesia, Persahabatan Hospital, Jl Persahabatan Raya 1, Jakarta 
      13230, Indonesia.
LA  - eng
GR  - 356/E4.1/AK.04.PT/202/Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi 
      Republik Indonesia (Ministry of Education, Culture, Research and Technology, 
      Republic of Indonesia), Southeast Asia Joint Funding Scheme for Research 
      Innovation/
PT  - Journal Article
DEP - 20211209
PL  - Switzerland
TA  - Vaccines (Basel)
JT  - Vaccines
JID - 101629355
PMC - PMC8704007
OTO - NOTNLM
OT  - HLA-A*24:07
OT  - SARS-CoV-2
OT  - T-cell epitopes
OT  - cytotoxic T-cells
OT  - helper T-cells
OT  - human leukocyte antigen
OT  - immunoinformatics
OT  - multi-epitope peptide-based vaccine
COIS- The authors declare no conflict of interest. The funders had no role in the 
      design of the study; in the collection, analyses, or interpretation of data; in 
      the writing of the manuscript, or in the decision to publish the results.
EDAT- 2021/12/29 06:00
MHDA- 2021/12/29 06:01
PMCR- 2021/12/09
CRDT- 2021/12/28 01:06
PHST- 2021/11/03 00:00 [received]
PHST- 2021/11/28 00:00 [revised]
PHST- 2021/11/30 00:00 [accepted]
PHST- 2021/12/28 01:06 [entrez]
PHST- 2021/12/29 06:00 [pubmed]
PHST- 2021/12/29 06:01 [medline]
PHST- 2021/12/09 00:00 [pmc-release]
AID - vaccines9121459 [pii]
AID - vaccines-09-01459 [pii]
AID - 10.3390/vaccines9121459 [doi]
PST - epublish
SO  - Vaccines (Basel). 2021 Dec 9;9(12):1459. doi: 10.3390/vaccines9121459.