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Shah M, Jaan S, Shehroz M, Sarfraz A, Asad K, Wara TU, Zaman A, Ullah R, Ali EA, Nishan U, Ojha SC. Deciphering the Immunogenicity of Monkeypox Proteins for Designing the Potential mRNA Vaccine. ACS Omega 2023; 8:43341-43355. [PMID: 38024731 PMCID: PMC10652822 DOI: 10.1021/acsomega.3c07866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
The Monkeypox virus (MPXV), an orthopox virus, is responsible for monkeypox in humans, a zoonotic disease similar to smallpox. This infection first appeared in the 1970s in humans and then in 2003, after which it kept on spreading all around the world. To date, various antivirals have been used to cure this disease, but now, MPXV has developed resistance against these, thus increasing the need for an alternative cure for this deadly disease. In this study, we devised a reverse vaccinology approach against MPXV using a messenger RNA (mRNA) vaccine by pinning down the antigenic proteins of this virus. By using bioinformatic tools, we predicted prospective immunogenic B and T lymphocyte epitopes. Based on cytokine inducibility score, nonallergenicity, nontoxicity, antigenicity, and conservancy, the final epitopes were selected. Our analysis revealed the stable structure of the mRNA vaccine and its efficient expression in host cells. Furthermore, strong interactions were demonstrated with toll-like receptors 2 (TLR2) and 4 (TLR4) according to the molecular dynamic simulation studies. The in silico immune simulation analyses revealed an overall increase in the immune responses following repeated exposure to the designed vaccine. Based on our findings, the vaccine candidate designed in this study has the potential to be tested as a promising novel mRNA therapeutic vaccine against MPXV infection.
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Affiliation(s)
- Mohibullah Shah
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Samavia Jaan
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
- School
of Biochemistry and Biotechnology, University
of the Punjab, Lahore 54590, Pakistan
| | - Muhammad Shehroz
- Department
of Bioinformatics, Kohsar University Murree, Murree 47150 Pakistan
| | - Asifa Sarfraz
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Khamna Asad
- School
of Biochemistry and Biotechnology, University
of the Punjab, Lahore 54590, Pakistan
| | - Tehreem Ul Wara
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Aqal Zaman
- Department
of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Riaz Ullah
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University Riyadh 11451, Saudi Arabia
| | - Essam A. Ali
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Umar Nishan
- Department
of Chemistry, Kohat University of Science
& Technology, Kohat 26000, Pakistan
| | - Suvash Chandra Ojha
- Department
of Infectious Diseases, The Affiliated Hospital
of Southwest Medical University, 646000 Luzhou, China
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Shah M, Anwar A, Qasim A, Jaan S, Sarfraz A, Ullah R, Ali EA, Nishan U, Shehroz M, Zaman A, Ojha SC. Proteome level analysis of drug-resistant Prevotella melaninogenica for the identification of novel therapeutic candidates. Front Microbiol 2023; 14:1271798. [PMID: 37808310 PMCID: PMC10556700 DOI: 10.3389/fmicb.2023.1271798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
The management of infectious diseases has become more critical due to the development of novel pathogenic strains with enhanced resistance. Prevotella melaninogenica, a gram-negative bacterium, was found to be involved in various infections of the respiratory tract, aerodigestive tract, and gastrointestinal tract. The need to explore novel drug and vaccine targets against this pathogen was triggered by the emergence of antimicrobial resistance against reported antibiotics to combat P. melaninogenica infections. The study involves core genes acquired from 14 complete P. melaninogenica strain genome sequences, where promiscuous drug and vaccine candidates were explored by state-of-the-art subtractive proteomics and reverse vaccinology approaches. A stringent bioinformatics analysis enlisted 18 targets as novel, essential, and non-homologous to humans and having druggability potential. Moreover, the extracellular and outer membrane proteins were subjected to antigenicity, allergenicity, and physicochemical analysis for the identification of the candidate proteins to design multi-epitope vaccines. Two candidate proteins (ADK95685.1 and ADK97014.1) were selected as the best target for the designing of a vaccine construct. Lead B- and T-cell overlapped epitopes were joined to generate potential chimeric vaccine constructs in combination with adjuvants and linkers. Finally, a prioritized vaccine construct was found to have stable interactions with the human immune cell receptors as confirmed by molecular docking and MD simulation studies. The vaccine construct was found to have cloning and expression ability in the bacterial cloning system. Immune simulation ensured the elicitation of significant immune responses against the designed vaccine. In conclusion, our study reported novel drug and vaccine targets and designed a multi-epitope vaccine against the P. melaninogenica infection. Further experimental validation will help open new avenues in the treatment of this multi-drug-resistant pathogen.
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Affiliation(s)
- Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Amna Anwar
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Aqsa Qasim
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Samavia Jaan
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Riaz Ullah
- Medicinal Aromatic and Poisonous Plants Research Center, College of Pharmacy King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science and Technology, Kohat, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree, Pakistan
| | - Aqal Zaman
- Department of Microbiology and Molecular Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Qasim A, Jaan S, Wara TU, Shehroz M, Nishan U, Shams S, Shah M, Ojha SC. Computer-aided genomic data analysis of drug-resistant Neisseria gonorrhoeae for the Identification of alternative therapeutic targets. Front Cell Infect Microbiol 2023; 13:1017315. [PMID: 37033487 PMCID: PMC10080061 DOI: 10.3389/fcimb.2023.1017315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Neisseria gonorrhoeae is an emerging multidrug resistance pathogen that causes sexually transmitted infections in men and women. The N. gonorrhoeae has demonstrated an emerging antimicrobial resistance against reported antibiotics, hence fetching the attention of researchers to address this problem. The present in-silico study aimed to find putative novel drug and vaccine targets against N. gonorrhoeae infection by the application of bioinformatics approaches. Core genes set of 69 N. gonorrhoeae strains was acquired from complete genome sequences. The essential and non-homologous metabolic pathway proteins of N. gonorrhoeae were identified. Moreover, different bioinformatics databases were used for the downstream analysis. The DrugBank database scanning identified 12 novel drug targets in the prioritized list. They were preferred as drug targets against this bacterium. A viable vaccine is unavailable so far against N. gonorrhoeae infection. In the current study, two outer-membrane proteins were prioritized as vaccine candidates via reverse vaccinology approach. The top lead B and T-cells overlapped epitopes were utilized to generate a chimeric vaccine construct combined with immune-modulating adjuvants, linkers, and PADRE sequences. The top ranked prioritized vaccine construct (V7) showed stable molecular interaction with human immune cell receptors as inferred during the molecular docking and MD simulation analyses. Considerable response for immune cells was interpreted by in-silico immune studies. Additional tentative validation is required to ensure the effectiveness of the prioritized vaccine construct against N. gonorrhoeae infection. The identified proteins can be used for further rational drug and vaccine designing to develop potential therapeutic entities against the multi-drug resistant N. gonorrhoeae.
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Affiliation(s)
- Aqsa Qasim
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Samavia Jaan
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Tehreem Ul Wara
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University, Murree, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
- *Correspondence: Suvash Chandra Ojha, ; Mohibullah Shah, ;
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Suvash Chandra Ojha, ; Mohibullah Shah, ;
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Jaan S, Shah M, Ullah N, Amjad A, Javed MS, Nishan U, Mustafa G, Nawaz H, Ahmed S, Ojha SC. Multi-epitope chimeric vaccine designing and novel drug targets prioritization against multi-drug resistant Staphylococcus pseudintermedius. Front Microbiol 2022; 13:971263. [PMID: 35992654 PMCID: PMC9386485 DOI: 10.3389/fmicb.2022.971263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
Biofilm synthesizing multi-drug resistant Staphylococcus pseudintermedius bacteria has been recognized as the human infectious agent. It has been detected in the diseases of skin, ear, and postoperative infections. Its infections are becoming a major health problem due to its multi-drug resistance capabilities. However, no commercial vaccine for the treatment of its infections is currently available in the market. Here we employed the subtractive proteomics and reverse vaccinology approach to determine the potential novel drug and vaccine targets against S. pseudintermedius infections in humans. After screening the core-proteome of the 39 complete genomes of S. pseudintermedius, 2 metabolic pathways dependent and 34 independent proteins were determined as novel potential drug targets. Two proteins were found and used as potential candidates for designing the chimeric vaccine constructs. Depending on the properties such as antigenicity, toxicity and solubility, multi-epitope based vaccines constructs were designed. For immunogenicity enhancement, different specific sequences like linkers, PADRE sequences and molecular adjuvants were added. Molecular docking and molecular dynamic simulation analyses were performed to evaluate the prioritized vaccine construct’s interactions with human immune cells HLA and TLR4. Finally, the cloning and expression ability of the vaccine construct was determined in the bacterial cloning system and human body immune response was predicted through immune simulation analysis. In conclusion, this study proposed the potential drug and vaccine targets and also designed a chimera vaccine to be tested and validated against infectious S. pseudintermedius species.
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Affiliation(s)
- Samavia Jaan
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
- *Correspondence: Mohibullah Shah, ;
| | - Najeeb Ullah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Adnan Amjad
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Sameem Javed
- Institute of Food Science and Nutrition, Bahauddin Zakariya University, Multan, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science and Technology, Kohat, Pakistan
| | - Ghazala Mustafa
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Haq Nawaz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Sarfraz Ahmed
- Department of Basic Sciences, University of Veterinary and Animal Sciences Lahore, Narowal, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Suvash Chandra Ojha,
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