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Bioengineering
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Tailored Peptide Modifications for Advanced Infection Control Strategies
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Tailored Peptide Modifications for Advanced Infection Control Strategies

A special issue of Bioengineering (ISSN 2306-5354). This special issue belongs to the section "Cellular and Molecular Bioengineering".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 7544

Special Issue Editors

Dr. Piyush Baindara

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Guest Editor
Animal Sciences Research Center, University of Missouri, Columbia, MO 65211, USA
Interests: antimicrobial peptides; infectious diseases; vaccines; anticancer; drug resistance
Dr. Ravinder Kumar

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Guest Editor
Department of Pathology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
Interests: yeast-based vaccine; virus like particles; yeast-based screening; industrial application of yeast; recombinant proteins
Dr. Santi Mandal

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Guest Editor
Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, WB, India
Interests: antimicrobial peptides; drug resistance; protein engineering; lipopeptides

Special Issue Information

Dear Colleagues,

While the world is already struggling with the rapid emergence of drug resistance and the scarcity of efficient antibiotics, the outbreak of new infectious agents such as SARS-CoV-2 increases the urgency of discovering new antimicrobial agents or strategies to fight against them. Tailored peptides including antimicrobial peptides (AMPs), peptide antibiotics, synthetic peptides, and peptide-based vaccines are recognized as potential alternatives to fight against drug resistance and new infections. Additionally, the synergistic action of AMPs with conventional antibiotics and their application as subunit vaccines or adjuvants is another approach to combat infections, as well as the further evolution of drug resistance.

In this Special Issue, authors are invited to submit original research, review articles, short communications, case series, and opinion papers related to, but not limited to, the following specific areas or research:

  1. Characterization and designing of novel AMPs, peptide antibiotics, synthetic peptides, and peptide-based vaccines or therapies.
  2. Strategies for the development of peptide-based therapies against infectious diseases.
  3. Peptide-based immunotherapies to combat cancer.
  4. Applications and strategies to use peptide-based therapies against autoimmune disease.
  5. Peptide-based therapies against fungal infections and antifungal drug resistance.
  6. Protein engineering strategies to design efficient peptide-based therapies.
  7. Synergistic action or combination treatment strategies of peptides with conventional antibiotics or other drugs to improve efficacy.
  8. New delivery strategies for peptides and peptide-based therapies to overcome drug resistance.
  9. Peptide-based therapies and immunotherapies in clinical trials and therapeutics.

Dr. Piyush Baindara
Dr. Ravinder Kumar
Dr. Santi Mandal
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Bioengineering is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • peptide-based vaccines
  • drug resistance
  • protein engineering
  • infectious diseases
  • antibacterial
  • antifungal
  • antiviral
  • immunotherapies
  • therapeutics

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Published Papers (3 papers)

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Research

21 pages, 5581 KiB  
Article
Reverse Vaccinology Integrated with Biophysics Techniques for Designing a Peptide-Based Subunit Vaccine for Bourbon Virus
by Taghreed N. Almanaa
Bioengineering 2024, 11(11), 1056; https://doi.org/10.3390/bioengineering11111056 - 23 Oct 2024
Cited by 1 | Viewed by 1485
Abstract
Despite the seriousness of the disease carried by ticks, little is known about the Bourbon virus. Only three US states have recorded human cases of Bourbon virus (BRBV) infection; in all cases, a tick bite was connected with the onset of the illness. [...] Read more.
Despite the seriousness of the disease carried by ticks, little is known about the Bourbon virus. Only three US states have recorded human cases of Bourbon virus (BRBV) infection; in all cases, a tick bite was connected with the onset of the illness. The Bourbon virus (BRBV) belongs to the Orthomyxoviridae family and Thogotovirus genus, originating in the states of the US, i.e., Kansas, Oklahoma and Missouri. The growing rates of BRBV infections in various parts of the US highlight the necessity for a thorough analysis of the virus’s transmission mechanisms, vector types and reservoir hosts. Currently, there are no vaccines or efficient antiviral therapies to stop these infections. It is imperative to produce a vaccination that is both affordable and thermodynamically stable to reduce the likelihood of future pandemics. Various computational techniques and reverse vaccinology methodologies were employed to identify specific B- and T-cell epitopes. After thorough examination, the linker proteins connected the B- and T-cell epitopes, resulting in this painstakingly constructed vaccine candidate. Furthermore, 3D modeling directed the vaccine construct toward molecular docking to determine its binding affinity and interaction with TLR-4. Human beta-defensin was used as an adjuvant and linked to the N-terminus to boost immunogenicity. Furthermore, the C-IMMSIM simulation resulted in high immunogenic activities, with activation of high interferon, interleukins and immunoglobulin. The results of the in silico cloning process for E. coli indicated that the vaccine construct will try its utmost to express itself in the host, with a codon adaptation CAI value of 0.94. A net binding free energy of −677.7 kcal/mol obtained during docking showed that the vaccine has a high binding affinity for immunological receptors. Further validation was achieved via molecular dynamic simulations, inferring the confirmational changes during certain time intervals, but the vaccine remained intact to the binding site for a 100 ns interval. The thermostability determined using an RMSF score predicted certain changes in the mechanistic insights of the loop region with carbon alpha deviations, but no major changes were observed during the simulations. Thus, the results obtained highlight a major concern for researchers to further validate the vaccine’s efficacy using in vitro and in vivo approaches. Full article
(This article belongs to the Special Issue Tailored Peptide Modifications for Advanced Infection Control Strategies)
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11 pages, 2348 KiB  
Article
CycP: A Novel Self-Assembled Vesicle-Forming Cyclic Antimicrobial Peptide to Control Drug-Resistant S. aureus
by Piyush Baindara, Dinata Roy and Santi M. Mandal
Bioengineering 2024, 11(8), 855; https://doi.org/10.3390/bioengineering11080855 - 21 Aug 2024
Cited by 3 | Viewed by 1559
Abstract
Antimicrobial peptides (AMPs) are considered a promising alternative to conventional antibiotics to fight against the rapid evolution of antibiotic resistance. Other than their potent antimicrobial properties, AMP-based vesicles can be used as efficient drug-delivery vehicles. In the present study, we synthesized and characterized [...] Read more.
Antimicrobial peptides (AMPs) are considered a promising alternative to conventional antibiotics to fight against the rapid evolution of antibiotic resistance. Other than their potent antimicrobial properties, AMP-based vesicles can be used as efficient drug-delivery vehicles. In the present study, we synthesized and characterized a new cyclic AMP, consisting of all-hydrophobic cores with antimicrobial activity against S. aureus. Interestingly, CycP undergoes supramolecular self-assembly, and self-assembled CycP (sCycP) vesicles are characterized under an electron microscope; however, these vesicles do not display antimicrobial activity. Next, sCycP vesicles are used in combination with SXT (sulfamethoxazole–trimethoprim) vesicles to check the drug loading and delivery capacity of sCycP vesicles to bacterial cell membranes. Interestingly, sCycP vesicles showed synergistic action with SXT vesicles and resulted in a significant reduction in MIC against S. aureus. Further, electron microscopy confirmed the membrane-specific killing mechanism of SXT-loaded sCycP vesicles. Additionally, CycP showed high binding affinities with the β-lactamase of S. aureus, which was one of its possible antimicrobial mechanisms of action. Overall, the results suggested that CycP is a novel self-assembled dual-action cyclic AMP with non-cytotoxic properties that can be used alone as an AMP or a self-assembled drug delivery vehicle for antibiotics to combat S. aureus infections. Full article
(This article belongs to the Special Issue Tailored Peptide Modifications for Advanced Infection Control Strategies)
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24 pages, 7165 KiB  
Article
Subtractive Proteomics and Reverse-Vaccinology Approaches for Novel Drug Target Identification and Chimeric Vaccine Development against Bartonella henselae Strain Houston-1
by Sudais Rahman, Chien-Chun Chiou, Shabir Ahmad, Zia Ul Islam, Tetsuya Tanaka, Abdulaziz Alouffi, Chien-Chin Chen, Mashal M. Almutairi and Abid Ali
Bioengineering 2024, 11(5), 505; https://doi.org/10.3390/bioengineering11050505 - 17 May 2024
Cited by 7 | Viewed by 3748
Abstract
Bartonella henselae is a Gram-negative bacterium causing a variety of clinical symptoms, ranging from cat-scratch disease to severe systemic infections, and it is primarily transmitted by infected fleas. Its status as an emerging zoonotic pathogen and its capacity to persist within host erythrocytes [...] Read more.
Bartonella henselae is a Gram-negative bacterium causing a variety of clinical symptoms, ranging from cat-scratch disease to severe systemic infections, and it is primarily transmitted by infected fleas. Its status as an emerging zoonotic pathogen and its capacity to persist within host erythrocytes and endothelial cells emphasize its clinical significance. Despite progress in understanding its pathogenesis, limited knowledge exists about the virulence factors and regulatory mechanisms specific to the B. henselae strain Houston-1. Exploring these aspects is crucial for targeted therapeutic strategies against this versatile pathogen. Using reverse-vaccinology-based subtractive proteomics, this research aimed to identify the most antigenic proteins for formulating a multi-epitope vaccine against the B. henselae strain Houston-1. One crucial virulent and antigenic protein, the PAS domain-containing sensor histidine kinase protein, was identified. Subsequently, the identification of B-cell and T-cell epitopes for the specified protein was carried out and the evaluated epitopes were checked for their antigenicity, allergenicity, solubility, MHC binding capability, and toxicity. The filtered epitopes were merged using linkers and an adjuvant to create a multi-epitope vaccine construct. The structure was then refined, with 92.3% of amino acids falling within the allowed regions. Docking of the human receptor (TLR4) with the vaccine construct was performed and demonstrated a binding energy of −1047.2 Kcal/mol with more interactions. Molecular dynamic simulations confirmed the stability of this docked complex, emphasizing the conformation and interactions between the molecules. Further experimental validation is necessary to evaluate its effectiveness against B. henselae. Full article
(This article belongs to the Special Issue Tailored Peptide Modifications for Advanced Infection Control Strategies)
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