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Naveed M, Mahmood S, Aziz T, Azeem A, Hussain I, Waseem M, Ali A, Alharbi M, Alshammari A, Alasmari AF. Designing a novel chimeric multi-epitope vaccine subunit against Staphylococcus argenteus through artificial intelligence approach integrating pan-genome analysis, in vitro identification, and immunogenicity profiling. J Biomol Struct Dyn 2023:1-16. [PMID: 37695632 DOI: 10.1080/07391102.2023.2256881] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Staphylococcus argenteus is a newly identified pathogen that causes respiratory tract infections, skin infections, such as cellulitis, abscesses, and impetigo, and currently, there is no licensed vaccine available against it. To develop a vaccine against S. argenteus, a bacterial pan-genome analysis was applied to identify potential vaccine candidates. A total of 4908 core proteins were retrieved and utilized for identifying four proteins, including SG38 Panton-Valentine leukocidin LukS-PV protein, SG62 staphylococcal enterotoxin type A protein, SG39 enterotoxin B protein, and SG43 enterotoxin type C3 protein as potential vaccine candidates. Epitopes were predicted for these proteins using different types of B and T-cell epitope prediction tools, and only those with a non-toxic profile, antigenic, non-allergenic, and immunogenic were selected. The selected epitopes were linked to each other to form a multi-epitope vaccine construct, which was further linked to the PADRE sequence (AKFVAAWTLKAAA) and 50s ribosomal L7/L12 protein to enhance the vaccine's antigenicity. The three-dimensional structure of the vaccine construct was assessed to determine its binding affinity with key Toll-like receptor 9 (TLR-9) and Toll-like receptor 5 (TLR-5) immune cell receptors. Our findings demonstrate that the vaccine exhibits favorable binding interactions with these immune cell receptors, indicating its potential efficacy. Molecular dynamic simulations further confirmed the accessibility of vaccine epitopes to the host immune system, substantiating its ability to elicit protective immune responses. Taken together, this study highlights the promising candidacy of the modeled vaccine construct for future in vivo and in vitro experimental investigations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Sarmad Mahmood
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Tariq Aziz
- Laboratory of Animal Health, Food Hygiene and Quality, Department of Agriculture, University of Ioannina, Arta, Greece
| | - Arooj Azeem
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Ibrar Hussain
- Punjab Health Facility Management Company, Chakwal, Pakistan
| | - Muhammad Waseem
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Ayaz Ali
- Department of Biotechnology, University of Malakand, Chakdara, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Rahman S, Nath S, Mohan U, Das AK. Targeting Staphylococcal Cell-Wall Biosynthesis Protein FemX Through Steered Molecular Dynamics and Drug-Repurposing Approach. ACS OMEGA 2023; 8:29292-29301. [PMID: 37599983 PMCID: PMC10433341 DOI: 10.1021/acsomega.3c02691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023]
Abstract
Staphylococcus aureus-mediated infection is a serious threat in this antimicrobial-resistant world. S. aureus has become a "superbug" by challenging conventional as well as modern treatment strategies. Nowadays, drug repurposing has become a new trend for the discovery of new drug molecules. This study focuses on evaluating FDA-approved drugs that can be repurposed against S. aureus infection. Steered molecular dynamics (SMD) has been performed for Lumacaftor and Olaparib against staphylococcal FemX to understand their binding to the active site. A time-dependent external force or rupture force has been applied to the ligands to calculate the force required to dislocate the ligand from the binding pocket. SMD analysis indicates that Lumacaftor has a high affinity for the substrate binding pocket in comparison to Olaparib. Umbrella sampling exhibits that Lumacaftor possesses a higher free energy barrier to displace it from the ligand-binding site. The bactericidal activity of Lumacaftor and Olaparib has been tested, and it shows that Lumacaftor has moderate activity along with biofilm inhibition potential (MIC value with conc. 128 μg/mL). Pharmacokinetic and toxicology evaluations indicate that Lumacaftor has higher pharmacokinetic potential with lower toxicity. This is the first experimental report where staphylococcal FemX has been targeted for the discovery of new drugs. It is suggested that Lumacaftor may be a potential lead molecule against S. aureus.
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Affiliation(s)
- Shakilur Rahman
- Department
of Biotechnology, Indian Institute of Technology
Kharagpur, Kharagpur, West Bengal 721302, India
| | - Subham Nath
- National
Institute of Pharmaceutical Education and Research Kolkata, Kolkata, West Bengal 700054, India
| | - Utpal Mohan
- National
Institute of Pharmaceutical Education and Research Kolkata, Kolkata, West Bengal 700054, India
| | - Amit Kumar Das
- Department
of Biotechnology, Indian Institute of Technology
Kharagpur, Kharagpur, West Bengal 721302, India
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Rahman S, Sarkar K, Das AK. Exploring staphylococcal superantigens to design a potential multi-epitope vaccine against Staphylococcus aureus: an in-silico reverse vaccinology approach. J Biomol Struct Dyn 2023; 41:13098-13112. [PMID: 36729064 DOI: 10.1080/07391102.2023.2171138] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023]
Abstract
Staphylococcus aureus is a horrifying bacteria capable of causing millions of deaths yearly across the globe. A major contribution to the success of S. aureus as an ESKAPE pathogen is the abundance of virulence factors that can manipulate the innate and adaptive immune system of the individual. Currently, no vaccine is available to treat S. aureus-mediated infections. In this study, we present in-silico approaches to design a stable, safe and immunogenic vaccine that could help to control the infections associated with the bacteria. Three vital pathogenic secreted toxins of S. aureus, such as staphylococcal enterotoxin A (SEA), staphylococcal enterotoxin B (SEB), Toxic-shock syndrome toxin (TSST-1), were selected using the reverse vaccinology approach to design the multi-epitope vaccine (MEV). Linear B-lymphocyte, cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes were predicted from these selected proteins. For designing the multi-epitope vaccine (MEV), B-cell epitopes were joined with the KK linker, CTL epitopes were joined with the AAY linker, and HTL epitopes were joined with the GPGPG linker. Finally, to increase the immune response to the vaccine, a human β-defensin-3 (hBD-3) adjuvant was added to the N-terminus of the MEV construct. The final MEV was found to be antigenic and non-allergen in nature. In-silico immune simulation and cloning analysis predicted the immune-stimulating potential of the designed MEV construct along with the cloning feasibility in the pET28a(+) vector with the E. coli expression system. This immunoinformatics study provides a platform for designing a suitable, safe and effective vaccine against S. aureus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shakilur Rahman
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Kasturi Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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Rahman S, Das AK. A subtractive proteomics and immunoinformatics approach towards designing a potential multi-epitope vaccine against pathogenic Listeriamonocytogenes. Microb Pathog 2022; 172:105782. [PMID: 36150556 DOI: 10.1016/j.micpath.2022.105782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/04/2022] [Accepted: 09/11/2022] [Indexed: 11/29/2022]
Abstract
Listeria monocytogenes is the causative agent of listeriosis, which is dangerous for pregnant women, the elderly or individuals with a weakened immune system. Individuals with leukaemia, cancer, HIV/AIDS, kidney transplant and steroid therapy suffer from immunological damage are menaced. World Health Organization (WHO) reports that human listeriosis has a high mortality rate of 20-30% every year. To date, no vaccine is available to treat listeriosis. Thereby, it is high time to design novel vaccines against L. monocytogenes. Here, we present computational approaches to design an antigenic, stable and safe vaccine against the L. monocytogenes that could help to control the infections associated with the pathogen. Three vital pathogenic proteins of L. monocytogenes, such as Listeriolysin O (LLO), Phosphatidylinositol-specific phospholipase C (PI-PLC), and Actin polymerization protein (ActA), were selected using a subtractive proteomics approach to design the multi-epitope vaccine (MEV). A total of 5 Cytotoxic T-lymphocyte (CTL) and 9 Helper T-lymphocyte (HTL) epitopes were predicted from these selected proteins. To design the multi-epitope vaccine (MEV) from the selected proteins, CTL epitopes were joined with the AAY linker, and HTL epitopes were joined with the GPGPG linker. Additionally, a human β-defensin-3 (hBD-3) adjuvant was added to the N-terminal side of the final MEV construct to increase the immune response to the vaccine. The final MEV was predicted to be antigenic, non-allergen and non-toxic in nature. Physicochemical property analysis suggested that the MEV construct is stable and could be easily purified through the E. coli expression system. This in-silico study showed that MEV has a robust binding interaction with Toll-like receptor 2 (TLR2), a key player in the innate immune system. Current subtractive proteomics and immunoinformatics study provides a background for designing a suitable, safe and effective vaccine against pathogenic L. monocytogenes.
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Affiliation(s)
- Shakilur Rahman
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
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Rahman S, Rajak K, Mishra S, Das AK. Identification of potential inhibitors against FemX of Staphylococcus aureus: A hierarchial in-silico drug repurposing approach. J Mol Graph Model 2022; 115:108215. [DOI: 10.1016/j.jmgm.2022.108215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 11/29/2022]
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Naorem RS, Pangabam BD, Bora SS, Goswami G, Barooah M, Hazarika DJ, Fekete C. Identification of Putative Vaccine and Drug Targets against the Methicillin-Resistant Staphylococcus aureus by Reverse Vaccinology and Subtractive Genomics Approaches. Molecules 2022; 27:2083. [PMID: 35408485 PMCID: PMC9000511 DOI: 10.3390/molecules27072083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 01/23/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen and responsible for causing life-threatening infections. The emergence of hypervirulent and multidrug-resistant (MDR) S. aureus strains led to challenging issues in antibiotic therapy. Consequently, the morbidity and mortality rates caused by S. aureus infections have a substantial impact on health concerns. The current worldwide prevalence of MRSA infections highlights the need for long-lasting preventive measures and strategies. Unfortunately, effective measures are limited. In this study, we focus on the identification of vaccine candidates and drug target proteins against the 16 strains of MRSA using reverse vaccinology and subtractive genomics approaches. Using the reverse vaccinology approach, 4 putative antigenic proteins were identified; among these, PrsA and EssA proteins were found to be more promising vaccine candidates. We applied a molecular docking approach of selected 8 drug target proteins with the drug-like molecules, revealing that the ZINC4235426 as potential drug molecule with favorable interactions with the target active site residues of 5 drug target proteins viz., biotin protein ligase, HPr kinase/phosphorylase, thymidylate kinase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase, and pantothenate synthetase. Thus, the identified proteins can be used for further rational drug or vaccine design to identify novel therapeutic agents for the treatment of multidrug-resistant staphylococcal infection.
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Affiliation(s)
- Romen Singh Naorem
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
| | - Bandana Devi Pangabam
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
| | - Sudipta Sankar Bora
- DBT—North East Centre for Agricultural Biotechnology (DBT-AAU Center), Assam Agricultural University, Jorhat 785013, India;
| | - Gunajit Goswami
- Multidisciplinary Research Unit, Jorhat Medical College and Hospital, Jorhat 785008, India;
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
- DBT—North East Centre for Agricultural Biotechnology (DBT-AAU Center), Assam Agricultural University, Jorhat 785013, India;
| | - Dibya Jyoti Hazarika
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, India; (M.B.); (D.J.H.)
| | - Csaba Fekete
- Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifusag utja. 6, 7624 Pecs, Hungary; (R.S.N.); (B.D.P.)
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Designing a novel in-silico multi-epitope vaccine against penicillin-binding protein 2A in Staphylococcus aureus. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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