2
|
Haq AU, Khan A, Khan J, Irum S, Waheed Y, Ahmad S, Nizam-Uddin N, Albutti A, Zaman N, Hussain Z, Ali SS, Waseem M, Kanwal F, Wei DQ, Wang Q. Annotation of Potential Vaccine Targets and Design of a Multi-Epitope Subunit Vaccine against Yersinia pestis through Reverse Vaccinology and Validation through an Agent-Based Modeling Approach. Vaccines (Basel) 2021; 9:vaccines9111327. [PMID: 34835260 PMCID: PMC8625334 DOI: 10.3390/vaccines9111327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 02/07/2023] Open
Abstract
Yersinia pestis is responsible for plague and major pandemics in Asia and Europe. This bacterium has shown resistance to an array of drugs commonly used for the treatment of plague. Therefore, effective therapeutics measurements, such as designing a vaccine that can effectively and safely prevent Y. pestis infection, are of high interest. To fast-track vaccine development against Yersinia pestis, herein, proteome-wide vaccine target annotation was performed, and structural vaccinology-assisted epitopes were predicted. Among the total 3909 proteins, only 5 (rstB, YPO2385, hmuR, flaA1a, and psaB) were shortlisted as essential vaccine targets. These targets were then subjected to multi-epitope vaccine design using different linkers. EAAK, AAY, and GPGPG as linkers were used to link CTL, HTL, and B-cell epitopes, and an adjuvant (beta defensin) was also added at the N-terminal of the MEVC. Physiochemical characterization, such as determination of the instability index, theoretical pI, half-life, aliphatic index, stability profiling, antigenicity, allergenicity, and hydropathy of the ensemble, showed that the vaccine is highly stable, antigenic, and non-allergenic and produces multiple interactions with immune receptors upon docking. In addition, molecular dynamics simulation confirmed the stable binding and good dynamic properties of the vaccine-TLR complex. Furthermore, in silico and immune simulation of the developed MEVC for Y. pestis showed that the vaccine triggered strong immune response after several doses at different intervals. Neutralization of the antigen was observed at the third day of injection. Conclusively, the vaccine designed here for Y. pestis produces an immune response; however, further immunological testing is needed to unveil its real efficacy.
Collapse
Affiliation(s)
- Azaz Ul Haq
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Jafar Khan
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Shamaila Irum
- Department of Zoology, University of Gujrat, Punjab 50700, Pakistan;
| | - Yasir Waheed
- Multidisciplinary Department, Foundation University Medical College, Foundation University Islamabad, Islamabad 44000, Pakistan;
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan;
| | - N. Nizam-Uddin
- Biomedical Engineering Department, HITEC University, Taxila 47080, Pakistan;
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
| | - Nasib Zaman
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Zahid Hussain
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, Kanju Campus, University of Swat, Swat 19200, Pakistan; (A.U.H.); (J.K.); (N.Z.); (Z.H.); (S.S.A.)
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad 46000, Pakistan;
| | - Fariha Kanwal
- Med-X Research Institute, School of Biomedical Engineering, Shanghai Jiaotong University, Shanghai 200240, China;
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Correspondence: (D.-Q.W.); (Q.W.)
| | - Qian Wang
- Department of Medicine, Nanjing Medical University, No. 140, Hanzhong Road, Nanjing 210029, China
- Correspondence: (D.-Q.W.); (Q.W.)
| |
Collapse
|
3
|
Yersinia pestis Plasminogen Activator. Biomolecules 2020; 10:biom10111554. [PMID: 33202679 PMCID: PMC7696990 DOI: 10.3390/biom10111554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 12/18/2022] Open
Abstract
The Gram-negative bacterium Yersinia pestis causes plague, a fatal flea-borne anthropozoonosis, which can progress to aerosol-transmitted pneumonia. Y. pestis overcomes the innate immunity of its host thanks to many pathogenicity factors, including plasminogen activator, Pla. This factor is a broad-spectrum outer membrane protease also acting as adhesin and invasin. Y. pestis uses Pla adhesion and proteolytic capacity to manipulate the fibrinolytic cascade and immune system to produce bacteremia necessary for pathogen transmission via fleabite or aerosols. Because of microevolution, Y. pestis invasiveness has increased significantly after a single amino-acid substitution (I259T) in Pla of one of the oldest Y. pestis phylogenetic groups. This mutation caused a better ability to activate plasminogen. In paradox with its fibrinolytic activity, Pla cleaves and inactivates the tissue factor pathway inhibitor (TFPI), a key inhibitor of the coagulation cascade. This function in the plague remains enigmatic. Pla (or pla) had been used as a specific marker of Y. pestis, but its solitary detection is no longer valid as this gene is present in other species of Enterobacteriaceae. Though recovering hosts generate anti-Pla antibodies, Pla is not a good subunit vaccine. However, its deletion increases the safety of attenuated Y. pestis strains, providing a means to generate a safe live plague vaccine.
Collapse
|
4
|
Wang X, Singh AK, Sun W. Protection and Safety Evaluation of Live Constructions Derived from the Pgm - and pPCP1 - Yersinia pestis Strain. Vaccines (Basel) 2020; 8:E95. [PMID: 32098032 PMCID: PMC7157699 DOI: 10.3390/vaccines8010095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
Based on a live attenuated Yersinia pestis KIM10(pCD1Ap) strain (Pgm-, pPCP1-), we attempted to engineer its lipid A species to achieve improvement of immunogenicity and safety. A mutant strain designated as YPS19(pCD1Ap), mainly synthesizing the hexa-acylated lipid A, and another mutant strain designated as YPS20(pCD1Ap), synthesizing 1-dephosphalated hexa-acylated lipid A (detoxified lipid A), presented relatively low virulence in comparison to KIM10(pCD1Ap) by intramuscular (i.m.) or subcutaneous (s.c.) administration. The i.m. administration with either the KIM10(pCD1Ap) or YPS19(pCD1Ap) strain afforded significant protection against bubonic and pneumonic plague compared to the s.c. administration, while administration with completely attenuated YPS20(pCD1Ap) strain failed to afford significant protection. Antibody analysis showed that i.m. administration induced balanced Th1 and Th2 responses but s.c. administration stimulated Th2-biased responses. Safety evaluation showed that YPS19(pCD1Ap) was relatively safer than its parent KIM10(pCD1Ap) in Hfe-/- mice manifesting iron overload in tissues, which also did not impair its protection. Therefore, the immune activity of hexa-acylated lipid A can be harnessed for rationally designing bacteria-derived vaccines.
Collapse
Affiliation(s)
| | | | - Wei Sun
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA; (X.W.); (A.K.S.)
| |
Collapse
|