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Cheukamud W, Chansap S, Rattanasroi K, Changklungmoa N, Kueakhai P. Construction and mouse antibody response evaluation of juvenile stage-specific chimeric protein from Fasciola gigantica. Vet Parasitol 2024; 331:110254. [PMID: 39047536 DOI: 10.1016/j.vetpar.2024.110254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/07/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024]
Abstract
Fasciolosis, caused by the liver fluke Fasciola gigantica, is a major parasitic disease that affects livestock and therefore causes significant economic losses in tropical countries. Although anthelminthic drugs can kill the parasite, drug-resistant liver fluke populations are increasing. In this study, a recombinant F. gigantica chimeric protein (rFgCHI) consisting of cathepsin L1H (FgCL1H), cathepsin B3 (FgCB3), and Saposin-like protein 1 (FgSAP1) was designed and expressed in Escherichia coli (BL21). The molecular weight of rFgCHI was 61 kDa. To study the antibody response, male BALB/c mice were immunized via the subcutaneous injection of rFgCHI combined with Quil A. Immunization with rFgCHI showed the induction of IgG1 and IgG2a with a higher IgG1 isotype level, indicating the potential of mixed Th1/Th2 immune responses, with Th2 predominating. However, the results showed high levels of IgG against the single proteins, except for rFgSAP1. Through Western blotting, mouse anti-rFgCHI polyclonal antibodies could be detected to the native proteins obtained from the parasite at all stages. Immunolocalization also revealed that the anti-rFgCHI antibodies could detect targeted antigens in the cecal epithelium of the parasite. These results demonstrated that rFgCHI is immunogenic to the mouse immune system and may potentially be a protein candidate for the development of a fasciolosis vaccine.
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Affiliation(s)
- Werachon Cheukamud
- Faculty of Allied Health Sciences and Research unit of vaccine and diagnosis of parasitic diseases, Burapha University, Long-Hard Bangsaen Road, Saen Sook Sub-district, Mueang District, Chonburi 20131, Thailand
| | - Supanan Chansap
- Faculty of Allied Health Sciences and Research unit of vaccine and diagnosis of parasitic diseases, Burapha University, Long-Hard Bangsaen Road, Saen Sook Sub-district, Mueang District, Chonburi 20131, Thailand
| | - Komsil Rattanasroi
- Faculty of Allied Health Sciences and Research unit of vaccine and diagnosis of parasitic diseases, Burapha University, Long-Hard Bangsaen Road, Saen Sook Sub-district, Mueang District, Chonburi 20131, Thailand
| | - Narin Changklungmoa
- Faculty of Allied Health Sciences and Research unit of vaccine and diagnosis of parasitic diseases, Burapha University, Long-Hard Bangsaen Road, Saen Sook Sub-district, Mueang District, Chonburi 20131, Thailand
| | - Pornanan Kueakhai
- Faculty of Allied Health Sciences and Research unit of vaccine and diagnosis of parasitic diseases, Burapha University, Long-Hard Bangsaen Road, Saen Sook Sub-district, Mueang District, Chonburi 20131, Thailand.
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2
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Jain PM, Nellikka A, Kammara R. Understanding bacteriocin heterologous expression: A review. Int J Biol Macromol 2024; 277:133916. [PMID: 39033897 DOI: 10.1016/j.ijbiomac.2024.133916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 07/12/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024]
Abstract
Bacteriocins are a diverse group of ribosomally synthesised antimicrobial peptides/proteins that play an important role in self-defence. They are widely used as bio-preservatives and effective substitutes for disease eradication. They can be used in conjunction with or as an alternative to antibiotics to minimize the risk of resistance development. There are remarkably few reports indicating resistance to bacteriocins. Although there are many research reports that emphasise heterologous expression of bacteriocin, there are no convincing reports on the significant role that intrinsic and extrinsic factors play in overexpression. A coordinated and cooperative expression system works in concert with multiple genetic elements encoding native proteins, immunoproteins, exporters, transporters and enzymes involved in the post-translational modification of bacteriocins. The simplest way could be to utilise the existing E. coli expression system, which is conventional, widely used for heterologous expression and has been further extended for bacteriocin expression. In this article, we will review the intrinsic and extrinsic factors, advantages, disadvantages and major problems associated with bacteriocin overexpression in E. coli. Finally, we recommend the most effective strategies as well as numerous bacteriocin expression systems from E. coli, Lactococcus, Kluveromyces lactis, Saccharomyces cerevisiae and Pichia pastoris for their suitability for successful overexpression.
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Affiliation(s)
- Priyanshi M Jain
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India
| | - Anagha Nellikka
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India
| | - Rajagopal Kammara
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India.
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3
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Rwere F, Cartee NMP, Yang Y, Waskell L. A flexible linker of 8-amino acids between the membrane binding segment and the FMN domain of cytochrome P450 reductase is necessary for optimal activity. J Inorg Biochem 2024; 259:112667. [PMID: 39032346 PMCID: PMC11298297 DOI: 10.1016/j.jinorgbio.2024.112667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
The diflavin NADPH-cytochrome P450 reductase (CYPOR) plays a critical role in human cytochrome P450 (CYP) activity by sequentially delivering two electrons from NADPH to CYP enzymes during catalysis. Although electron transfer to forty-eight human CYP enzymes by the FMN hydroquinone of CYPOR is well-known, the role of the linker between the NH2-terminus membrane-binding domain (MBD) and FMN domain in supporting the activity of P450 enzymes remains poorly understood. Here we demonstrate that a linker with at least eight residues is required to form a functional CYPOR-CYP2B4 complex. The linker has been shortened in two amino-acid increments from Phe44 to Ile57 using site directed mutagenesis. The ability of the deletion mutants to support cytochrome P450 2B4 (CYP2B4) catalysis and reduce ferric CYP2B4 was determined using an in vitro assay and stopped-flow spectrophotometry. Steady-state enzyme kinetics showed that shortening the linker by 8-14 amino acids inhibited (63-99%) the ability of CYPOR to support CYP2B4 activity and significantly increased the Km of CYPOR for CYP2B4. In addition, the reductase mutants decreased the rate of reduction of ferric CYP2B4 (46-95%) compared to wildtype when the linker was shortened by 8-14 residues. These results indicate that a linker with a minimum length of eight residues is necessary to enable the FMN domain of reductase to interact with CYP2B4 to form a catalytically competent complex. Our study provides evidence that the length of the MBD-FMN domain linker is a major determinant of the ability of CYPOR to support CYP catalysis and drug metabolism by P450 enzymes. PREAMBLE: This manuscript is dedicated in memory of Dr. James R. Kincaid who was the doctoral advisor to Dr. Freeborn Rwere and a longtime collaborator and friend of Dr. Lucy Waskell. Dr. James R. Kincaid was a distinguished professor of chemistry specializing in resonance Raman (rR) studies of heme proteins. He inspired Dr. Rwere (a Zimbabwean native) and three other Zimbabweans (Dr. Remigio Usai, Dr. Daniel Kaluka and Ms. Munyaradzi E. Manyumwa) to use lasers to document subtle changes occurring at heme active site of globin proteins (myoglobin and hemoglobin) and cytochrome P450 enzymes. Dr. Rwere appreciate his contributions to the development of talented Black scientists from Africa.
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Affiliation(s)
- Freeborn Rwere
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI, USA; Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, 3174 Porter Dr, Palo Alto, CA, USA.
| | - Naw May P Cartee
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI, USA
| | - Yuting Yang
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI, USA
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan and VAMC, 2215 Fuller Road, Ann Arbor, MI, USA
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4
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Schultes FPJ, Welter L, Schmidtke M, Tischler D, Mügge C. A tailored cytochrome P450 monooxygenase from Gordonia rubripertincta CWB2 for selective aliphatic monooxygenation. Biol Chem 2024:hsz-2024-0041. [PMID: 39331465 DOI: 10.1515/hsz-2024-0041] [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: 03/07/2024] [Accepted: 09/04/2024] [Indexed: 09/28/2024]
Abstract
Cytochrome P450 monooxygenases are recognized as versatile biocatalysts due to their broad reaction capabilities. One important reaction is the hydroxylation of non-activated C-H bonds. The subfamily CYP153A is known for terminal hydroxylation reactions, giving access to functionalized aliphatics. Whilst fatty derivatives may be converted by numerous enzyme classes, midchain aliphatics are seldomly accepted, a prime property of CYP153As. We report here on a new CYP153A member from the genome of the mesophilic actinobacterium Gordonia rubripertincta CWB2 as an efficient biocatalyst. The gene was overexpressed in Escherichia coli and fused with a surrogate electron transport system from Acinetobacter sp. OC4. This chimeric self-sufficient whole-cell system could perform hydroxylation and epoxidation reactions: conversions of C6-C14 alkanes, alkenes, alcohols and of cyclic compounds were observed, yielding production rates of, e.g., 2.69 mM h-1 for 1-hexanol and 4.97 mM h-1 for 1,2-epoxyhexane. Optimizing the linker compositions between the protein units led to significantly altered activity. Balancing linker length and flexibility with glycine-rich and helix-forming linker units increased 1-hexanol production activity to 350 % compared to the initial linker setup with entirely helical linkers. The study shows that strategic coupling of efficient electron supply and a selective enzyme enables previously challenging monooxygenation reactions of midchain aliphatics.
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Affiliation(s)
- Fabian Peter Josef Schultes
- Microbial Biotechnology, Faculty of Biology and Biotechnology, 9142 Ruhr University Bochum , D-44801 Bochum, Germany
| | - Leon Welter
- Microbial Biotechnology, Faculty of Biology and Biotechnology, 9142 Ruhr University Bochum , D-44801 Bochum, Germany
| | - Myra Schmidtke
- Microbial Biotechnology, Faculty of Biology and Biotechnology, 9142 Ruhr University Bochum , D-44801 Bochum, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Faculty of Biology and Biotechnology, 9142 Ruhr University Bochum , D-44801 Bochum, Germany
| | - Carolin Mügge
- Microbial Biotechnology, Faculty of Biology and Biotechnology, 9142 Ruhr University Bochum , D-44801 Bochum, Germany
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5
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Huang PJ, Lin YL, Chen CH, Lin HY, Fang SC. A chloroplast sulphate transporter modulates glutathione-mediated redox cycling to regulate cell division. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39189939 DOI: 10.1111/pce.15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024]
Abstract
Glutathione redox cycling is important for cell cycle regulation, but its mechanisms are not well understood. We previously identified a small-sized mutant, suppressor of mat3 15-1 (smt15-1) that has elevated cellular glutathione. Here, we demonstrated that SMT15 is a chloroplast sulphate transporter. Reducing expression of γ-GLUTAMYLCYSTEINE SYNTHETASE, encoding the rate-limiting enzyme required for glutathione biosynthesis, corrected the size defect of smt15-1 cells. Overexpressing GLUTATHIONE SYNTHETASE (GSH2) recapitulated the small-size phenotype of smt15-1 mutant, confirming the role of glutathione in cell division. Hence, SMT15 may regulate chloroplast sulphate concentration to modulate cellular glutathione levels. In wild-type cells, glutathione and/or thiol-containing molecules (GSH/thiol) accumulated in the cytosol at the G1 phase and decreased as cells entered the S/M phase. While the cytosolic GSH/thiol levels in the small-sized mutants, smt15-1 and GSH2 overexpressors, mirrored those of wild-type cells (accumulating during G1 and declining at early S/M phase), GSH/thiol was specifically accumulated in the basal bodies at early S/M phase in the small-sized mutants. Therefore, we propose that GSH/thiol-mediated redox signalling in the basal bodies may regulate mitotic division number in Chlamydomonas reinhardtii. Our findings suggest a new mechanism by which glutathione regulates the multiple fission cell cycle in C. reinhardtii.
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Affiliation(s)
- Pin-Jui Huang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Yen-Ling Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsiang-Yin Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
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6
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Arshad NF, Nordin FJ, Foong LC, In LLA, Teo MYM. Engineering receptor-binding domain and heptad repeat domains towards the development of multi-epitopes oral vaccines against SARS-CoV-2 variants. PLoS One 2024; 19:e0306111. [PMID: 39146295 PMCID: PMC11326571 DOI: 10.1371/journal.pone.0306111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 06/11/2024] [Indexed: 08/17/2024] Open
Abstract
The inability of existing vaccines to cope with the mutation rate has highlighted the need for effective preventative strategies for COVID-19. Through the secretion of immunoglobulin A, mucosal delivery of vaccines can effectively stimulate mucosal immunity for better protection against SARS-CoV-2 infection. In this study, various immunoinformatic tools were used to design a multi-epitope oral vaccine against SARS-CoV-2 based on its receptor-binding domain (RBD) and heptad repeat (HR) domains. T and B lymphocyte epitopes were initially predicted from the RBD and HR domains of SARS-CoV-2, and potential antigenic, immunogenic, non-allergenic, and non-toxic epitopes were identified. Epitopes that are highly conserved and have no significant similarity to human proteome were selected. The epitopes were joined with appropriate linkers, and an adjuvant was added to enhance the vaccine efficacy. The vaccine 3D structure constructs were docked with toll-like receptor 4 (TLR-4) and TLR1-TLR2, and the binding affinity was calculated. The designed multi-epitope vaccine construct (MEVC) consisted of 33 antigenic T and B lymphocyte epitopes. The results of molecular dockings and free binding energies confirmed that the MEVC effectively binds to TLR molecules, and the complexes were stable. The results suggested that the designed MEVC is a potentially safe and effective oral vaccine against SARS-CoV-2. This in silico study presents a novel approach for creating an oral multi-epitope vaccine against the rapidly evolving SARS-CoV-2 variants. These findings offer valuable insights for developing an effective strategy to combat COVID-19. Further preclinical and clinical studies are required to confirm the efficacy of the MEVC vaccine.
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Affiliation(s)
- Nur Farhanah Arshad
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Fariza Juliana Nordin
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Lian Chee Foong
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Michelle Yee Mun Teo
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
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7
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Giacomoni J, Åkerblom M, Habekost M, Fiorenzano A, Kajtez J, Davidsson M, Parmar M, Björklund T. Identification and validation of novel engineered AAV capsid variants targeting human glia. Front Neurosci 2024; 18:1435212. [PMID: 39193523 PMCID: PMC11348808 DOI: 10.3389/fnins.2024.1435212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 07/15/2024] [Indexed: 08/29/2024] Open
Abstract
Direct neural conversion of endogenous non-neuronal cells, such as resident glia, into therapeutic neurons has emerged as a promising strategy for brain repair, aiming to restore lost or damaged neurons. Proof-of-concept has been obtained from animal studies, yet these models do not efficiently recapitulate the complexity of the human brain, and further refinement is necessary before clinical translation becomes viable. One important aspect is the need to achieve efficient and precise targeting of human glial cells using non-integrating viral vectors that exhibit a high degree of cell type specificity. While various naturally occurring or engineered adeno-associated virus (AAV) serotypes have been utilized to transduce glia, efficient targeting of human glial cell types remains an unsolved challenge. In this study, we employ AAV capsid library engineering to find AAV capsids that selectively target human glia in vitro and in vivo. We have identified two families of AAV capsids that induce efficient targeting of human glia both in glial spheroids and after glial progenitor cell transplantation into the rat forebrain. Furthermore, we show the robustness of this targeting by transferring the capsid peptide from the parent AAV2 serotype onto the AAV9 serotype, which facilitates future scalability for the larger human brain.
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Affiliation(s)
- Jessica Giacomoni
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Malin Åkerblom
- Molecular Neuromodulation, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Mette Habekost
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Alessandro Fiorenzano
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Janko Kajtez
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Marcus Davidsson
- Molecular Neuromodulation, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Malin Parmar
- Developmental and Regenerative Neurobiology, Lund Stem Cell Center, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - Tomas Björklund
- Molecular Neuromodulation, Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
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8
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Mendes G, Faulk B, Kaparthi B, Irion AR, Fong BL, Bayless K, Bondos SE. Genetic Functionalization of Protein-Based Biomaterials via Protein Fusions. Biomacromolecules 2024; 25:4639-4662. [PMID: 39074364 PMCID: PMC11323028 DOI: 10.1021/acs.biomac.4c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024]
Abstract
Proteins implement many useful functions, including binding ligands with unparalleled affinity and specificity, catalyzing stereospecific chemical reactions, and directing cell behavior. Incorporating proteins into materials has the potential to imbue devices with these desirable traits. This review highlights recent advances in creating active materials by genetically fusing a self-assembling protein to a functional protein. These fusion proteins form materials while retaining the function of interest. Key advantages of this approach include elimination of a separate functionalization step during materials synthesis, uniform and dense coverage of the material by the functional protein, and stabilization of the functional protein. This review focuses on macroscale materials and discusses (i) multiple strategies for successful protein fusion design, (ii) successes and limitations of the protein fusion approach, (iii) engineering solutions to bypass any limitations, (iv) applications of protein fusion materials, including tissue engineering, drug delivery, enzyme immobilization, electronics, and biosensing, and (v) opportunities to further develop this useful technique.
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Affiliation(s)
- Gabriela
Geraldo Mendes
- Department
of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health, Bryan, Texas 77807-3260, United States
- Fralin
Biomedical Research Institute, Virginia
Tech University, Roanoke, Virginia 24016, United States
| | - Britt Faulk
- Department
of Medical Physiology, College of Medicine, Texas A&M Health, Bryan, Texas 77807, United States
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas 77843, United States
| | - Bhavika Kaparthi
- Department
of Medical Physiology, College of Medicine, Texas A&M Health, Bryan, Texas 77807, United States
| | - Andrew R. Irion
- Department
of Medical Physiology, College of Medicine, Texas A&M Health, Bryan, Texas 77807, United States
| | - Brandon Look Fong
- Department
of Medical Physiology, College of Medicine, Texas A&M Health, Bryan, Texas 77807, United States
| | - Kayla Bayless
- Department
of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health, Bryan, Texas 77807-3260, United States
- Department
of Medical Physiology, College of Medicine, Texas A&M Health, Bryan, Texas 77807, United States
| | - Sarah E. Bondos
- Department
of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health, Bryan, Texas 77807-3260, United States
- Department
of Medical Physiology, College of Medicine, Texas A&M Health, Bryan, Texas 77807, United States
- Department
of BioSciences, Rice University, Houston, Texas 77005, United States
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9
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Zhou Z, Zhu F, Ma S, Tan C, Yang H, Zhang P, Xu Y, Qin R, Luo Y, Chen J, Pan P. Design of Cryptococcus neoformans multi-epitope vaccine based on immunoinformatics method. Med Mycol 2024; 62:myae080. [PMID: 39122658 DOI: 10.1093/mmy/myae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/01/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024] Open
Abstract
Cryptococcus neoformans is a widely distributed opportunistic pathogenic fungus. While C. neoformans commonly infects immunocompromised individuals, it can also affect those who are immunocompetent. Transmission of C. neoformans primarily occurs through the respiratory tract, leading to the development of meningitis. The mortality rate of Cryptococcal meningitis is high, and treatment options are limited. Cryptococcus neoformans infections pose a significant public health threat and currently lack targeted and effective response strategies. This study aimed to screen T lymphocyte (cytotoxic T lymphocyte and helper T lymphocyte) and B lymphocyte epitopes derived from four C. neoformans antigens and develop two multi-epitope vaccines by combining them with various adjuvants. Molecular docking results demonstrated that the vaccines bind stably to Toll-like receptor 4 ( and induce innate immunity. The credibility of the molecular docking results was validated through subsequent molecular dynamics simulations. Furthermore, the results of immune simulation analyses underscored the multi-epitope vaccine's capability to effectively induce robust humoral and cellular immune responses within the host organism. These two vaccines have demonstrated theoretical efficacy against C. neoformans infection as indicated by computer analysis. Nevertheless, additional experimental validation is essential to substantiate the protective efficacy of the vaccines.
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Affiliation(s)
- Ziyou Zhou
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Yizhong Xu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Rongliu Qin
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Yuying Luo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
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10
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Gao J, Jing J, Shang G, Chen C, Duan M, Yu W, Wang K, Luo J, Song M, Chen K, Chen C, Zhang T, Ding D. TDRD1 phase separation drives intermitochondrial cement assembly to promote piRNA biogenesis and fertility. Dev Cell 2024:S1534-5807(24)00395-2. [PMID: 39029469 DOI: 10.1016/j.devcel.2024.06.017] [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: 01/19/2024] [Revised: 05/22/2024] [Accepted: 06/20/2024] [Indexed: 07/21/2024]
Abstract
The intermitochondrial cement (IMC) is a prominent germ granule that locates among clustered mitochondria in mammalian germ cells. Serving as a key platform for Piwi-interacting RNA (piRNA) biogenesis; however, how the IMC assembles among mitochondria remains elusive. Here, we identify that Tudor domain-containing 1 (TDRD1) triggers IMC assembly via phase separation. TDRD1 phase separation is driven by the cooperation of its tetramerized coiled-coil domain and dimethylarginine-binding Tudor domains but is independent of its intrinsically disordered region. TDRD1 is recruited to mitochondria by MILI and sequentially enhances mitochondrial clustering and triggers IMC assembly via phase separation to promote piRNA processing. TDRD1 phase separation deficiency in mice disrupts IMC assembly and piRNA biogenesis, leading to transposon de-repression and spermatogenic arrest. Moreover, TDRD1 phase separation is conserved in vertebrates but not in invertebrates. Collectively, our findings demonstrate a role of phase separation in germ granule formation and establish a link between membrane-bound organelles and membrane-less organelles.
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Affiliation(s)
- Jie Gao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiongjie Jing
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200127, China
| | - Guanyi Shang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Canmei Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Maoping Duan
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wenyang Yu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Ke Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jie Luo
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Manxiu Song
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Kun Chen
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200127, China
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Deqiang Ding
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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11
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Sehgal A, Sharma D, Kaushal N, Gupta Y, Martynova E, Kabwe E, Chandy S, Rizvanov A, Khaiboullina S, Baranwal M. Designing a Conserved Immunogenic Peptide Construct from the Nucleocapsid Protein of Puumala orthohantavirus. Viruses 2024; 16:1030. [PMID: 39066193 PMCID: PMC11281540 DOI: 10.3390/v16071030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/09/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Puumala orthohantavirus (PUUV) is an emerging zoonotic virus endemic to Europe and Russia that causes nephropathia epidemica, a mild form of hemorrhagic fever with renal syndrome (HFRS). There are limited options for treatment and diagnosis of orthohantavirus infection, making the search for potential immunogenic candidates crucial. In the present work, various bioinformatics tools were employed to design conserved immunogenic peptides containing multiple epitopes of PUUV nucleocapsid protein. Eleven conserved peptides (90% conservancy) of the PUUV nucleocapsid protein were identified. Three conserved peptides containing multiple T and B cell epitopes were selected using a consensus epitope prediction algorithm. Molecular docking using the HPEP dock server demonstrated strong binding interactions between the epitopes and HLA molecules (ten alleles for each class I and II HLA). Moreover, an analysis of population coverage using the IEDB database revealed that the identified peptides have over 90% average population coverage across six continents. Molecular docking and simulation analysis reveal a stable interaction with peptide constructs of chosen immunogenic peptides and Toll-like receptor-4. These computational analyses demonstrate selected peptides' immunogenic potential, which needs to be validated in different experimental systems.
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Affiliation(s)
- Ayushi Sehgal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
| | - Diksha Sharma
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
| | - Neha Kaushal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
| | - Yogita Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
| | - Ekaterina Martynova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia; (E.M.); (E.K.); (S.K.)
| | - Emmanuel Kabwe
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia; (E.M.); (E.K.); (S.K.)
| | - Sara Chandy
- Childs Trust Medical Research Foundation (CTMRF) Kanchi, Chennai 600034, India;
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia; (E.M.); (E.K.); (S.K.)
| | - Svetlana Khaiboullina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia; (E.M.); (E.K.); (S.K.)
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
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12
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Kaur B, Karnwal A, Bansal A, Malik T. An Immunoinformatic-Based In Silico Identification on the Creation of a Multiepitope-Based Vaccination Against the Nipah Virus. BIOMED RESEARCH INTERNATIONAL 2024; 2024:4066641. [PMID: 38962403 PMCID: PMC11221950 DOI: 10.1155/2024/4066641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 07/05/2024]
Abstract
The zoonotic viruses pose significant threats to public health. Nipah virus (NiV) is an emerging virus transmitted from bats to humans. The NiV causes severe encephalitis and acute respiratory distress syndrome, leading to high mortality rates, with fatality rates ranging from 40% to 75%. The first emergence of the disease was found in Malaysia in 1998-1999 and later in Bangladesh, Cambodia, Timor-Leste, Indonesia, Singapore, Papua New Guinea, Vietnam, Thailand, India, and other South and Southeast Asian nations. Currently, no specific vaccines or antiviral drugs are available. The potential advantages of epitope-based vaccines include their ability to elicit specific immune responses while minimizing potential side effects. The epitopes have been identified from the conserved region of viral proteins obtained from the UniProt database. The selection of conserved epitopes involves analyzing the genetic sequences of various viral strains. The present study identified two B cell epitopes, seven cytotoxic T lymphocyte (CTL) epitopes, and seven helper T lymphocyte (HTL) epitope interactions from the NiV proteomic inventory. The antigenic and physiological properties of retrieved protein were analyzed using online servers ToxinPred, VaxiJen v2.0, and AllerTOP. The final vaccine candidate has a total combined coverage range of 80.53%. The tertiary structure of the constructed vaccine was optimized, and its stability was confirmed with the help of molecular simulation. Molecular docking was performed to check the binding affinity and binding energy of the constructed vaccine with TLR-3 and TLR-5. Codon optimization was performed in the constructed vaccine within the Escherichia coli K12 strain, to eliminate the danger of codon bias. However, these findings must require further validation to assess their effectiveness and safety. The development of vaccines and therapeutic approaches for virus infection is an ongoing area of research, and it may take time before effective interventions are available for clinical use.
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Affiliation(s)
- Beant Kaur
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Arun Karnwal
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Anu Bansal
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Tabarak Malik
- Department of Biomedical SciencesInstitute of HealthJimma University, Jimma, Ethiopia
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13
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Lindner C, Friemel A, Schwegler N, Timmermann L, Pham TL, Reusche V, Kovermann M, Thomas F. Thermostable WW-Domain Scaffold to Design Functional β-Sheet Miniproteins. J Am Chem Soc 2024. [PMID: 38853610 DOI: 10.1021/jacs.4c03498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
There has been a recent surge in the design of miniproteins for medicinal chemistry, biomaterial design, or synthetic biology. In particular, there is an interest in peptide scaffolds that fold reliably, predictably, and with solid stability. In this article, we present the design of a highly thermostable WW domain, a three-stranded β-sheet motif, with a superior melting temperature of about 90 °C to serve as a core scaffold onto which receptor-like properties can be grafted. We have performed specific rounds of sequence iteration on a WW-domain consensus sequence to decipher sequence positions that affect structural and, thus, thermal stability. We identified a sequence-structure relationship that yields a highly thermostable WW-domain scaffold. High-resolution NMR spectroscopy was applied, which enabled the identification of structural features at the atomic scale that contribute to this high thermostability. Finally, we grafted the binding motifs of the three WW-domain groups─Group I, Group II/III, and Group IV─and organophosphate and metal binding onto the highly thermostable WW-domain scaffold and obtained thermostable de novo WW domains that indeed display the different binding modes that were intended. The organophosphate-binding WW domains exhibit melting temperatures that are up to 34 K higher than previously reported top-down designs. These results impressively demonstrate that the highly thermostable WW-domain core scaffold is a solid platform for the design of discrete and reliably folding functional β-sheet peptide miniproteins, providing an essential addition to the toolbox of peptide scaffolds previously used in synthetic biology and material design.
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Affiliation(s)
- Christina Lindner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Anke Friemel
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Niklas Schwegler
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Lisa Timmermann
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Vanessa Reusche
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Michael Kovermann
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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14
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Huang Y, Chen Z, Lan J, Zhang L, Chen H, Jiang L, Yu H, Liu N, Liao C, Han Q. MDR49 coding for both P-glycoprotein and TMOF transporter functions in ivermectin resistance, trypsin activity inhibition, and fertility in the yellow fever mosquito, Aedes aegypti. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 201:105899. [PMID: 38685208 DOI: 10.1016/j.pestbp.2024.105899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/30/2024] [Accepted: 04/06/2024] [Indexed: 05/02/2024]
Abstract
This study investigated the function of the MDR49 gene in Aedes aegypti. MDR49 mutants were constructed using CRISPR/Cas9 technology; the mutation led to increased sensitivity to ivermectin (LC50: from 1.3090 mg L-1 to 0.5904 mg L-1), and a reduction in midgut trypsin activity. These findings suggest that the P-gp encoded by MDR49 confers resistance to ivermectin and impacts the reproductive function in Ae. aegypti. RNA interference technology showed that knockdown of MDR49 gene resulted in a significant decrease in the expression of VGA1 after a blood meal, as well as a decrease in the number of eggs laid and their hatching rate. LC-MS revealed that following ivermectin treatment, the MDR493d+2s/3d+2s strain larvae exhibited significantly higher drug concentrations in the head and fat body compared to the wild type. Modeling of inward-facing P-gp and molecular docking found almost no difference in the affinity of P-gp for ivermectin before and after the mutation. However, modeling of the outward-facing conformation demonstrated that the flexible linker loop between TM5 and TM6 of P-gp undergoes changes after the mutation, resulting in a decrease in trypsin activity and an increase in sensitivity to ivermectin. These results provide useful insights into ivermectin resistance and the other roles played by the MDR49 gene.
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Affiliation(s)
- Yuqi Huang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Zhaohui Chen
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Jianqiang Lan
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Lei Zhang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Huaqing Chen
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Linlong Jiang
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Hongxiao Yu
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China
| | - Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36830, USA
| | - Chenghong Liao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China.
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life and Health Sciences, Hainan University, Haikou, Hainan 570228, China; One Health Institute, Hainan University, Haikou, Hainan 570228, China.
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15
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Su J, Xiao Y, Wei L, Lei H, Sun F, Wang W, Yin J, Xiong R, Li S, Zhang P, Zhou Y, Wang X, Zheng J, Wang JZ. Generation of tau dephosphorylation-targeting chimeras for the treatment of Alzheimer's disease and related tauopathies. Sci Bull (Beijing) 2024; 69:1137-1152. [PMID: 38341350 DOI: 10.1016/j.scib.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/06/2023] [Accepted: 01/08/2024] [Indexed: 02/12/2024]
Abstract
Abnormal hyperphosphorylation and accumulation of tau protein play a pivotal role in neurodegeneration in Alzheimer's disease (AD) and many other tauopathies. Selective elimination of hyperphosphorylated tau is promising for the therapy of these diseases. We have conceptualized a strategy, named dephosphorylation-targeting chimeras (DEPTACs), for specifically hijacking phosphatases to tau to debilitate its hyperphosphorylation. Here, we conducted the step-by-step optimization of each constituent motif to generate DEPTACs with reasonable effectiveness in facilitating the dephosphorylation and subsequent clearance of pathological tau. Specifically, for one of the selected chimeras, D16, we demonstrated its significant efficiency in rescuing the neurodegeneration caused by neurotoxic K18-tau seeds in vitro. Moreover, intravenous administration of D16 also alleviated tau pathologies in the brain and improved memory deficits in AD mice. These results suggested DEPTACs as targeted modulators of tau phosphorylation, which hold therapeutic potential for AD and other tauopathies.
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Affiliation(s)
- Jingfen Su
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yue Xiao
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Linyu Wei
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Sino-UK Joint Laboratory of Brain Function and Injury of Henan Province, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Huiyang Lei
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Fei Sun
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weixia Wang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Yin
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430030, China
| | - Rui Xiong
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shihong Li
- Department of Anesthesiology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Pei Zhang
- The Core Facility and Technical Support, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430030, China
| | - Ying Zhou
- Research Center for Medicine and Structural Biology, Wuhan University, Wuhan 430030, China
| | - Xiaochuan Wang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jie Zheng
- Neuroscience Research Institute and Department of Neurobiology, School of Basic Medical Sciences, Peking University, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission, Beijing 100083, China.
| | - Jian-Zhi Wang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Education Ministry of China/Hubei Province for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226000, China.
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16
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Akter A, Ananna NF, Ullah H, Islam S, Al Amin M, Kibria KMK, Mahmud S. Computational approach for identifying immunogenic epitopes and optimizing peptide vaccine through in-silico cloning against Mycoplasma genitalium. Heliyon 2024; 10:e28223. [PMID: 38596014 PMCID: PMC11002066 DOI: 10.1016/j.heliyon.2024.e28223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
Mycoplasma genitalium is a pathogenic microorganism linked to a variety of severe health conditions including ovarian cancer, prostate cancer, HIV transmission, and sexually transmitted diseases. A more effective approach to address the challenges posed by this pathogen, given its high antibiotic resistance rates, could be the development of a peptide vaccine. In this study, we used experimentally validated 13 membrane proteins and their immunogenicity to identify suitable vaccine candidates. Thus, based on immunogenic properties and high conservation among other Mycoplasma genitalium sub-strains, the P110 surface protein is considered for further investigation. Later on, we identified T-cell epitopes and B-cell epitopes from the P110 protein to construct a multiepitope-based vaccine. As a result, the 'NIAPISFSFTPFTAA' T-cell epitope and 'KVKYESSGSNNISFDS' B-cell epitope have shown 99.53% and 87.50% population coverage along with 100% conservancy among the subspecies, and both epitopes were found to be non-allergenic. Furthermore, focusing on molecular docking analysis showed the lowest binding energy for MHC-I (-137.5 kcal/mol) and MHC-II (-183.3 kcal/mol), leading to a satisfactory binding strength between the T-cell epitopes and the MHC molecules. However, the constructed multiepitope vaccine (MEV) consisting of 54 amino acids demonstrates favorable characteristics for a vaccine candidate, including a theoretical pI of 4.25 with a scaled solubility of 0.812 and high antigenicity probabilities. Additionally, structural analyses reveal that the MEV displays substantial alpha helices and extended strands, vital for its immunogenicity. Molecular docking with the human Toll-like receptors TLR1/2 heterodimer shows strong binding affinity, reinforcing its potential to elicit an immune response. Our immune simulation analysis demonstrates immune memory development and robust immunity, while codon adaptation suggests optimal expression in E. coli using the pET-28a(+) vector. These findings collectively highlight the MEV's potential as a valuable vaccine candidate against M. genitalium.
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Affiliation(s)
- Asma Akter
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Natasha Farhin Ananna
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Hedayet Ullah
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Sirajul Islam
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Md Al Amin
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - K M Kaderi Kibria
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Shahin Mahmud
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
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17
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Miyanabe K, Yamashita T, Tsumoto K. Thermodynamic and molecular dynamic insights into how fusion influences peptide-tag recognition of an antibody. Sci Rep 2024; 14:8685. [PMID: 38622354 PMCID: PMC11018781 DOI: 10.1038/s41598-024-59355-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
To understand the effect of protein fusion on the recognition of a peptide-tag by an antibody, we fused a CCR5-derived peptide-tag (pep1) to GFP and investigated its recognition by an anti-pep1 antibody, 4B08. First, to characterize the thermodynamic properties associated with the pep1-4B08 binding, isothermal titration calorimetry experiments were conducted. It was found that pep1 fused to the C-terminus of GFP (GFP-CT) enhanced the enthalpic gain by 2.1 kcal mol-1 and the entropic loss only by 0.9 kcal mol-1, resulting in an 8-fold increase in the binding affinity compared to the unfused pep1. On the other hand, pep1 fused to the N-terminus of GFP (GFP-NT) enhanced the enthalpic gain by 3.0 kcal mol-1 and the entropic loss by 3.2 kcal mol-1, leading to no significant enhancement of the binding affinity. To gain deeper insights, molecular dynamics simulations of GFP-NT, GFP-CT, and pep1 were performed. The results showed that the location of the fusion point sensitively affects the interaction energy, the solvent accessible surface area, and the fluctuation of pep1 in the unbound state, which explains the difference in the experimental thermodynamic properties.
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Affiliation(s)
- Kazuhiro Miyanabe
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takefumi Yamashita
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
- Department of Physical Chemistry, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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18
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Robang A, Roy A, Dodd-o JB, He D, Le JV, McShan AC, Hu Y, Kumar VA, Paravastu AK. Structural Consequences of Introducing Bioactive Domains to Designer β-Sheet Peptide Self-Assemblies. Biomacromolecules 2024; 25:1429-1438. [PMID: 38408372 PMCID: PMC10934295 DOI: 10.1021/acs.biomac.3c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
We applied solid- and solution-state nuclear magnetic resonance spectroscopy to examine the structure of multidomain peptides composed of self-assembling β-sheet domains linked to bioactive domains. Bioactive domains can be selected to stimulate specific biological responses (e.g., via receptor binding), while the β-sheets provide the desirable nanoscale properties. Although previous work has established the efficacy of multidomain peptides, molecular-level characterization is lacking. The bioactive domains are intended to remain solvent-accessible without being incorporated into the β-sheet structure. We tested for three possible anticipated molecular-level consequences of introducing bioactive domains to β-sheet-forming peptides: (1) the bioactive domain has no effect on the self-assembling peptide structure; (2) the bioactive domain is incorporated into the β-sheet nanofiber; and (3) the bioactive domain interferes with self-assembly such that nanofibers are not formed. The peptides involved in this study incorporated self-assembling domains based on the (SL)6 motif and bioactive domains including a VEGF-A mimic (QK), an IGF-mimic (IGF-1c), and a de novo SARS-CoV-2 binding peptide (SBP3). We observed all three of the anticipated outcomes from our examination of peptides, illustrating the unintended structural effects that could adversely affect the desired biofunctionality and biomaterial properties of the resulting peptide hydrogel. This work is the first attempt to evaluate the structural effects of incorporating bioactive domains into a set of peptides unified by a similar self-assembling peptide domain. These structural insights reveal unmet challenges in the design of highly tunable bioactive self-assembling peptide hydrogels.
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Affiliation(s)
- Alicia
S. Robang
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Abhishek Roy
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Dongjing He
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Justin V. Le
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andrew C. McShan
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Yuhang Hu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vivek A. Kumar
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemicals and Materials Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Biology, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Anant K. Paravastu
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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19
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Chen P, Ye M, Chen Y, Wang Q, Wang Q, Zhong M. Dual-transgenic BiFC vector systems for protein-protein interaction analysis in plants. Front Genet 2024; 15:1355568. [PMID: 38525241 PMCID: PMC10957565 DOI: 10.3389/fgene.2024.1355568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Protein-protein interaction (PPI) play a pivotal role in cellular signal transduction. The bimolecular fluorescence complementation (BiFC) assay offers a rapid and intuitive means to ascertain the localization and interactions of target proteins within living cells. BiFC is based on fluorescence complementation by reconstitution of a functional fluorescent protein by co-expression of N- and C-terminal fragments of this protein. When fusion proteins interact, the N- and C-terminal fragments come into close proximity, leading to the reconstitution of the fluorescent protein. In the conventional approach, the N-terminal and C-terminal fragments of the fluorescent protein are typically expressed using two separate vectors, which largely relies on the efficiency of the transformation of the two vectors in the same cells. Furthermore, issues of vector incompatibility can often result in loss of one plasmid. To address these challenges, we have developed novel dual-transgenic BiFC vectors, designed as pDTQs, derived from the previously published pDT1 vector. This set of BiFC vectors offers the following advantages: 1) Both fluorescent fusion proteins are expressed sequentially within a single vector, enhancing expression efficiency; 2) Independent promoters and terminators regulate the expression of the two proteins potentially mitigating vector compatibility issues; 3) A long linker is inserted between the fluorescent protein fragment and the gene of interest, facilitating the recombination of the fused fluorescent protein into an active form; 4) Four distinct types of fluorescent proteins, namely, EYFP, mVenus, mRFP1Q66T and mCherry are available for BiFC analysis. We assessed the efficiency of the pDTQs system by investigating the oligomerization of Arabidopsis CRY2 and CRY2-BIC2 interactions in N. benthamiana. Notably, the pDTQs were found to be applicable in rice, underscoring their potential utility across various plant species.
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Affiliation(s)
| | | | | | | | | | - Ming Zhong
- College of Agriculture, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
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20
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Zhang Y, Mariz FC, Sehr P, Spagnoli G, Koenig KM, Çelikyürekli S, Kreuziger T, Zhao X, Bolchi A, Ottonello S, Müller M. Inter-epitope spacer variation within polytopic L2-based human papillomavirus antigens affects immunogenicity. NPJ Vaccines 2024; 9:44. [PMID: 38402256 PMCID: PMC10894200 DOI: 10.1038/s41541-024-00832-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/05/2024] [Indexed: 02/26/2024] Open
Abstract
The human papillomavirus minor capsid protein L2 is being extensively explored in pre-clinical studies as an attractive vaccine antigen capable of inducing broad-spectrum prophylactic antibody responses. Recently, we have developed two HPV vaccine antigens - PANHPVAX and CUT-PANHPVAX- both based on heptameric nanoparticle antigens displaying polytopes of the L2 major cross-neutralizing epitopes of eight mucosal and twelve cutaneous HPV types, respectively. Prompted by the variable neutralizing antibody responses against some of the HPV types targeted by the antigens observed in previous studies, here we investigated the influence on immunogenicity of six distinct glycine-proline spacers inserted upstream to a specific L2 epitope. We show that spacer variants differentially influence antigen immunogenicity in a mouse model, with the antigen constructs M8merV6 and C12merV6 displaying a superior ability in the induction of neutralizing antibodies as determined by pseudovirus-based neutralization assays (PBNAs). L2-peptide enzyme-linked immunosorbent assay (ELISA) assessments determined the total anti-L2 antibody level for each antigen variant, showing for the majority of sera a correlation with their repective neutralizing antibody level. Surface Plasmon Resonance revealed that L2 epitope-specific, neutralizing monoclonal antibodies (mAbs) display distinct avidities to different antigen spacer variants. Furthermore, mAb affinity toward individual spacer variants was well correlated with their neutralizing antibody induction capacity, indicating that the mAb affinity assay predicts L2-based antigen immunogenicity. These observations provide insights on the development and optimization of L2-based HPV vaccines.
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Affiliation(s)
- Yueru Zhang
- German Cancer Research Center, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Filipe Colaco Mariz
- German Cancer Research Center, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Peter Sehr
- EMBL-DKFZ Chemical Biology Core Facility, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Gloria Spagnoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Karl Moritz Koenig
- German Cancer Research Center, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Simay Çelikyürekli
- German Cancer Research Center, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Tim Kreuziger
- Ruprecht-Karls University Heidelberg, Heidelberg, Germany
| | - Xueer Zhao
- German Cancer Research Center, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Angelo Bolchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Simone Ottonello
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124, Parma, Italy
| | - Martin Müller
- German Cancer Research Center, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany.
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21
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Aldoukhi AH, Bilalis P, Alhattab DM, Valle-Pérez AU, Susapto HH, Pérez-Pedroza R, Backhoff-García E, Alsawaf SM, Alshehri S, Boshah H, Alrashoudi AA, Aljabr WA, Alaamery M, Alrashed M, Hasanato RM, Farzan RA, Alsubki RA, Moretti M, Abedalthagafi MS, Hauser CAE. Fusing Peptide Epitopes for Advanced Multiplex Serological Testing for SARS-CoV-2 Antibody Detection. ACS BIO & MED CHEM AU 2024; 4:37-52. [PMID: 38404747 PMCID: PMC10885102 DOI: 10.1021/acsbiomedchemau.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 02/27/2024]
Abstract
The tragic COVID-19 pandemic, which has seen a total of 655 million cases worldwide and a death toll of over 6.6 million seems finally tailing off. Even so, new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to arise, the severity of which cannot be predicted in advance. This is concerning for the maintenance and stability of public health, since immune evasion and increased transmissibility may arise. Therefore, it is crucial to continue monitoring antibody responses to SARS-CoV-2 in the general population. As a complement to polymerase chain reaction tests, multiplex immunoassays are elegant tools that use individual protein or peptide antigens simultaneously to provide a high level of sensitivity and specificity. To further improve these aspects of SARS-CoV-2 antibody detection, as well as accuracy, we have developed an advanced serological peptide-based multiplex assay using antigen-fused peptide epitopes derived from both the spike and the nucleocapsid proteins. The significance of the epitopes selected for antibody detection has been verified by in silico molecular docking simulations between the peptide epitopes and reported SARS-CoV-2 antibodies. Peptides can be more easily and quickly modified and synthesized than full length proteins and can, therefore, be used in a more cost-effective manner. Three different fusion-epitope peptides (FEPs) were synthesized and tested by enzyme-linked immunosorbent assay (ELISA). A total of 145 blood serum samples were used, compromising 110 COVID-19 serum samples from COVID-19 patients and 35 negative control serum samples taken from COVID-19-free individuals before the outbreak. Interestingly, our data demonstrate that the sensitivity, specificity, and accuracy of the results for the FEP antigens are higher than for single peptide epitopes or mixtures of single peptide epitopes. Our FEP concept can be applied to different multiplex immunoassays testing not only for SARS-CoV-2 but also for various other pathogens. A significantly improved peptide-based serological assay may support the development of commercial point-of-care tests, such as lateral-flow-assays.
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Affiliation(s)
- Ali H. Aldoukhi
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Panayiotis Bilalis
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Dana M. Alhattab
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Alexander U. Valle-Pérez
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Hepi H. Susapto
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Rosario Pérez-Pedroza
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Emiliano Backhoff-García
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sarah M. Alsawaf
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Salwa Alshehri
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Hattan Boshah
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Abdulelah A. Alrashoudi
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Waleed A. Aljabr
- Research
Centre, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Manal Alaamery
- Developmental
Medicine Department, King Abdullah International Medical Research
Center, King Abdulaziz Medical City, Ministry of National Guard-Health
Affairs, King Saud Bin Abdulaziz University
for Health Sciences, Riyadh 11426, Saudi Arabia
- KACST-BWH
Centre of Excellence for Biomedicine, Joint Centers of Excellence
Program, King Abdulaziz City for Science
and Technology (KACST), Riyadh 12371, Saudi Arabia
- Saudi
Human Genome Project (SHGP), Satellite Lab at King Abdulaziz Medical
City (KAMC), Ministry of National Guard Health Affairs (MNG-HA), King Abdulaziz City for Science and Technology (KACST), Riyadh 11426, Saudi Arabia
| | - May Alrashed
- Department
of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
- Chair
of Medical and Molecular Genetics Research, King Saud University, Riyadh 11433, Saudi Arabia
| | - Rana M. Hasanato
- Department
of Pathology and Laboratory Medicine, King
Saud University, Riyadh 11433, Saudi Arabia
| | - Raed A. Farzan
- Department
of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
- Chair
of Medical and Molecular Genetics Research, King Saud University, Riyadh 11433, Saudi Arabia
| | - Roua A. Alsubki
- Department
of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
- Chair
of Medical and Molecular Genetics Research, King Saud University, Riyadh 11433, Saudi Arabia
| | - Manola Moretti
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
| | - Malak S. Abedalthagafi
- Pathology and Laboratory Medicine, Emory
School of Medicine, Atlanta, Georgia 30329, United States
| | - Charlotte A. E. Hauser
- Laboratory
for Nanomedicine, Division of Biological and Environmental Science
and Engineering (BESE), King Abdullah University
of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Computational
Bioscience Research Center (CBRC), King
Abdullah University of Science and Technology, Thuwal 23955-69900, Saudi Arabia
- Red Sea
Research Center, Division of Biological and Environmental
Science and Engineering (BESE), King Abdullah
University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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22
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Park JM, Kim JH, Kim G, Sim HJ, Ahn SM, Choi KS, Kwon HJ. Rapid Antibacterial Activity Assessment of Chimeric Lysins. Int J Mol Sci 2024; 25:2430. [PMID: 38397110 PMCID: PMC10888538 DOI: 10.3390/ijms25042430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024] Open
Abstract
Various chimeric lysins have been developed as efficacious antibiotics against multidrug-resistant bacteria, but direct comparisons of their antibacterial activities have been difficult due to the preparation of multiple recombinant chimeric lysins. Previously, we reported an Escherichia coli cell-free expression method to better screen chimeric lysins against Staphylococcus aureus, but we still needed to increase the amounts of expressed proteins enough to be able to detect them non-isotopically for quantity comparisons. In this study, we improved the previous cell-free expression system by adding a previously reported artificial T7 terminator and reversing the different nucleotides between the T7 promoter and start codon to those of the T7 phage. The new method increased the expressed amount of chimeric lysins enough for us to detect them using Western blotting. Therefore, the qualitative comparison of activity between different chimeric lysins has become possible via the adjustment of the number of variables between samples without protein purification. We applied this method to select more active chimeric lysins derived from our previously reported chimeric lysin (ALS2). Finally, we compared the antibacterial activities of our selected chimeric lysins with reported chimeric lysins (ClyC and ClyO) and lysostaphin and determined the rank orders of antibacterial activities on different Staphylococcus aureus strains in our experimental conditions.
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Affiliation(s)
- Jin-Mi Park
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
| | - Jun-Hyun Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
| | - Gun Kim
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Pharmacology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hun-Ju Sim
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Pharmacology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun-Min Ahn
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
| | - Kang-Seuk Choi
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyuk-Joon Kwon
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
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23
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Ninyio N, Schmitt K, Sergon G, Nilsson C, Andersson S, Scherbak N. Stable expression of HIV-1 MPER extended epitope on the surface of the recombinant probiotic bacteria Escherichia Coli Nissle 1917 using CRISPR/Cas9. Microb Cell Fact 2024; 23:39. [PMID: 38311724 PMCID: PMC10840157 DOI: 10.1186/s12934-023-02290-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/28/2023] [Indexed: 02/06/2024] Open
Abstract
BACKGROUND Mucosal vaccines have the potential to induce protective immune responses at the sites of infection. Applying CRISPR/Cas9 editing, we aimed to develop a probiotic-based vaccine candidate expressing the HIV-1 envelope membrane-proximal external region (MPER) on the surface of E. coli Nissle 1917. RESULTS The HIV-1 MPER epitope was successfully introduced in the porin OmpF of the E. coli Nissle 1917 (EcN-MPER) and the modification was stable over 30 passages of the recombinant bacteria on the DNA and protein level. Furthermore, the introduced epitope was recognized by a human anti-HIV-1 gp41 (2F5) antibody using both live and heat-killed EcN-MPER, and this antigenicity was also retained over 30 passages. Whole-cell dot blot suggested a stronger binding of anti-HIV-1 gp41 (2F5) to heat-killed EcN-MPER than their live counterpart. An outer membrane vesicle (OMV) - rich extract from EcN-MPER culture supernatant was equally antigenic to anti-HIV-1 gp41 antibody which suggests that the MPER antigen could be harboured in EcN-MPER OMVs. Using quantitative ELISA, we determined the amount of MPER produced by the modified EcN to be 14.3 µg/108 cfu. CONCLUSIONS The CRISPR/Cas9 technology was an effective method for establishment of recombinant EcN-MPER bacteria that was stable over many passages. The developed EcN-MPER clone was devoid of extraneous plasmids and antibiotic resistance genes which eliminates the risk of plasmid transfer to animal hosts, should this clone be used as a vaccine. Also, the EcN-MPER clone was recognised by anti-HIV-1 gp41 (2F5) both as live and heat-killed bacteria making it suitable for pre-clinical evaluation. Expression of OmpF on bacterial surfaces and released OMVs identifies it as a compelling candidate for recombinant epitope modification, enabling surface epitope presentation on both bacteria and OMVs. By applying the methods described in this study, we present a potential platform for cost-effective and rational vaccine antigen expression and administration, offering promising prospects for further research in the field of vaccine development.
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Affiliation(s)
- Nathaniel Ninyio
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Katharina Schmitt
- School of Science and Technology, Life Science Center, Örebro University, Örebro, Sweden
- Institute of Virology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Gladys Sergon
- School of Science and Technology, Life Science Center, Örebro University, Örebro, Sweden
| | - Charlotta Nilsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Sören Andersson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Public Health Analysis and Data Management, Unit for Vaccination Programmes, Public Health Agency of Sweden, Solna, Sweden
| | - Nikolai Scherbak
- School of Science and Technology, Life Science Center, Örebro University, Örebro, Sweden.
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24
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Garg A, González-Foutel NS, Gielnik MB, Kjaergaard M. Design of functional intrinsically disordered proteins. Protein Eng Des Sel 2024; 37:gzae004. [PMID: 38431892 DOI: 10.1093/protein/gzae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/22/2023] [Indexed: 03/05/2024] Open
Abstract
Many proteins do not fold into a fixed three-dimensional structure, but rather function in a highly disordered state. These intrinsically disordered proteins pose a unique challenge to protein engineering and design: How can proteins be designed de novo if not by tailoring their structure? Here, we will review the nascent field of design of intrinsically disordered proteins with focus on applications in biotechnology and medicine. The design goals should not necessarily be the same as for de novo design of folded proteins as disordered proteins have unique functional strengths and limitations. We focus on functions where intrinsically disordered proteins are uniquely suited including disordered linkers, desiccation chaperones, sensors of the chemical environment, delivery of pharmaceuticals, and constituents of biomolecular condensates. Design of functional intrinsically disordered proteins relies on a combination of computational tools and heuristics gleaned from sequence-function studies. There are few cases where intrinsically disordered proteins have made it into industrial applications. However, we argue that disordered proteins can perform many roles currently performed by organic polymers, and that these proteins might be more designable due to their modularity.
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Affiliation(s)
- Ankush Garg
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | | | - Maciej B Gielnik
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
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25
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van Zyl EM, Coburn JM. Functionalization of Bacterial Cellulose with the Antimicrobial Peptide KR-12 via Chimerical Cellulose-Binding Peptides. Int J Mol Sci 2024; 25:1462. [PMID: 38338739 PMCID: PMC10855235 DOI: 10.3390/ijms25031462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Bacterial-derived cellulose (BC) has been studied as a promising material for biomedical applications, including wound care, due to its biocompatibility, water-holding capacity, liquid/gas permeability, and handleability properties. Although BC has been studied as a dressing material for cutaneous wounds, to date, BC inherently lacks antibacterial properties. The current research utilizes bifunctional chimeric peptides containing carbohydrate binding peptides (CBP; either a short version or a long version) and an antimicrobial peptide (AMP), KR-12. The secondary structure of the chimeric peptides was evaluated and confirmed that the α-helix structure of KR-12 was retained for both chimeric peptides evaluated (Long-CBP-KR12 and Short-CBP-KR12). Chimeric peptides and their individual components were assessed for cytotoxicity, where only higher concentrations of Short-CBP and longer timepoints of Short-CBP-KR12 exposure exhibited negative effects on metabolic activity, which was attributed to solubility issues. All KR-12-containing peptides exhibited antibacterial activity in solution against Escherichia coli (E. coli) and Pseudomonas aeruginosa (P. aeruginosa). The lipopolysaccharide (LPS) binding capability of the peptides was evaluated and the Short-CBP-KR12 peptide exhibited enhanced LPS-binding capabilities compared to KR-12 alone. Both chimeric peptides were able to bind to BC and were observed to be retained on the surface over a 7-day period. All functionalized materials exhibited no adverse effects on the metabolic activity of both normal human dermal fibroblasts (NHDFs) and human epidermal keratinocyte (HaCaT) epithelial cells. Additionally, the BC tethered chimeric peptides exhibited antibacterial activity against E. coli. Overall, this research outlines the design and evaluation of chimeric CBP-KR12 peptides for developing antimicrobial BC membranes with potential applications in wound care.
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Affiliation(s)
| | - Jeannine M. Coburn
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, USA
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Lacerna N, Cong Y, Schmidt EW. An Autocatalytic Peptide Cyclase Improves Fidelity and Yield of Circular Peptides In Vivo and In Vitro. ACS Synth Biol 2024; 13:394-401. [PMID: 38194299 PMCID: PMC10804404 DOI: 10.1021/acssynbio.3c00645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Peptide cyclization improves conformational rigidity, providing favorable pharmacological properties, such as proteolytic resistance, target specificity, and membrane permeability. Thus, many synthetic and biosynthetic peptide circularization strategies have been developed. PatG and related natural macrocyclases process diverse peptide sequences, generating millions of cyclic derivatives. However, the application of these cyclases is limited by low yields and the potential presence of unwanted intermediates. Here, we designed a covalently fused G macrocyclase with substrates that efficiently and spontaneously release cyclic peptides. To increase the fidelity of synthesis, we developed an orthogonal control mechanism enabling precision synthesis in Escherichia coli. As a result, a library comprising 4.8 million cyclic derivatives was constructed, producing an estimated 2.6 million distinct cyclic peptides with an improved yield and fidelity.
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Affiliation(s)
- Noel Lacerna
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ying Cong
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, United States
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Sam S, Ofoghi H, Farahmand B. Developing of SARS-CoV-2 fusion protein expressed in E. coli Shuffle T7 for enhanced ELISA detection sensitivity - an integrated experimental and bioinformatic approach. J Biomol Struct Dyn 2024:1-16. [PMID: 38234051 DOI: 10.1080/07391102.2024.2302941] [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: 07/24/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
In the recent COVID-19 pandemic, developing effective diagnostic assays is crucial for controlling the spread of the SARS-CoV-2 virus. Multi-domain fusion proteins are a promising approach to detecting SARS-CoV-2 antibodies. In this study, we designed an antigen named CoV2-Pro, containing two RBD domains from SARS-CoV-2 Omicron and Delta variants and one CTD domain of the nucleoprotein in the order of RBD-RBD-N, linked by a super flexible glycine linker. We evaluated the suitability of E. coli Shuffle T7 and BL21 (DE3) strain for expressing CoV2-Pro. Moreover, Bioinformatic studies were conducted first to analyze the tertiary structure of CoV2-Pro. The CoV2-Pro sequences were cloned into a pET-32b (+) vector for expression in E. coli Shuffle T7 and BL21 (DE3). SDS-PAGE and western blot confirmed the protein expression and folding structure. The CoV2-Pro-TRX was purified by Ni-NTA affinity chromatography. Dot blot analysis was performed to evaluate the antigenic characterization of the CoV2-Pro. A molecular docking simulation was conducted to assess the binding affinity of CoV2-Pro with LY-COV555 (Bamlanivimab) monoclonal antibody. A molecular dynamic was performed to analyze the stability of the structure. Bioinformatic and experimental studies revealed a stable conformational 3D structure of the CoV2-Pro. The CoV2-Pro interacted with SARS-CoV-2 antibodies, confirming the correct antigenic structure. We assert with confidence that CoV2-Pro is ideal for developing an ELISA assay for precise diagnosis and rigorous vaccine evaluation during the COVID-19 prevalence.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sohrab Sam
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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Hossen MS, Hasan MN, Haque M, Al Arian T, Halder SK, Uddin MJ, Abdullah-Al-Mamun M, Shakil MS. Immunoinformatics-aided rational design of multiepitope-based peptide vaccine (MEBV) targeting human parainfluenza virus 3 (HPIV-3) stable proteins. J Genet Eng Biotechnol 2023; 21:162. [PMID: 38055114 DOI: 10.1186/s43141-023-00623-5] [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: 07/14/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Human parainfluenza viruses (HPIVs) are common RNA viruses responsible for respiratory tract infections. Human parainfluenza virus 3 (HPIV-3) is particularly pathogenic, causing severe illnesses with no effective vaccine or therapy available. RESULTS The current study employed a systematic immunoinformatic/reverse vaccinology approach to design a multiple epitope-based peptide vaccine against HPIV-3 by analyzing the virus proteome. On the basis of a number of therapeutic features, all three stable and antigenic proteins with greater immunological relevance, namely matrix protein, hemagglutinin neuraminidase, and RNA-directed RNA polymerase L, were chosen for predicting and screening suitable T-cell and B-cell epitopes. All of our desired epitopes exhibited no homology with human proteins, greater population coverage (99.26%), and high conservancy among reported HPIV-3 isolates worldwide. All of the T- and B-cell epitopes are then joined by putative ligands, yielding a 478-amino acid-long final construct. Upon computational refinement, validation, and thorough screening, several programs rated our peptide vaccine as biophysically stable, antigenic, allergenic, and non-toxic in humans. The vaccine protein demonstrated sufficiently stable interaction as well as binding affinity with innate immune receptors TLR3, TLR4, and TLR8. Furthermore, codon optimization and virtual cloning of the vaccine sequence in a pET32a ( +) vector showed that it can be readily expressed in the bacterial system. CONCLUSION The in silico designed HPIV-3 vaccine demonstrated potential in evoking an effective immune response. This study paves the way for further preclinical and clinical evaluation of the vaccine, offering hope for a future solution to combat HPIV-3 infections.
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Affiliation(s)
- Md Sakib Hossen
- Department of Biochemistry and Molecular Biology, Primeasia University, Banani, Dhaka, 1213, Bangladesh.
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh.
| | - Md Nazmul Hasan
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh.
- Department of Biochemistry and Molecular Biology, Hajee Mohammad Danesh Science and Technology University, Dinajpur, 5200, Bangladesh.
| | - Munima Haque
- Biotechnology Program, Department of Mathematics and Natural Sciences (MNS), Brac University, kha-208, 1 Bir Uttam Rafiqul Islam Ave, Dhaka, 1212, Bangladesh
| | - Tawsif Al Arian
- Department of Pharmacy, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Sajal Kumar Halder
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Jasim Uddin
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - M Abdullah-Al-Mamun
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Salman Shakil
- Division of Computer Aided Drug Design, BioAid, Mirpur, Dhaka, 1216, Bangladesh
- Microbiology Program, Department of Mathematics and Natural Sciences (MNS), Brac University, 66 Mohakhali, Dhaka, 1212, Bangladesh
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29
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Cheng C, Zhao Z, Liu G. Expression, Purification, and Crystallization of the Vγ9Vδ2 T-cell Receptor Recognizing Protein/Peptide Antigens. Protein J 2023; 42:778-791. [PMID: 37620608 DOI: 10.1007/s10930-023-10151-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2023] [Indexed: 08/26/2023]
Abstract
γδ T cells, especially Vγ9Vδ2 T cells, play an important role in mycobacterial infection. We have identified some Vγ9Vδ2 T cells that recognize protein/peptide antigens derived from mycobacteria, which may induce protective immune responses to mycobacterial infection. To clarify the structural basis of the molecular recognition mechanism, we tried many methods to express the Vγ9Vδ2 T-cell receptor (TCR). The Vγ9Vδ2 TCR was not expressed well in a prokaryotic expression system or a baculovirus expression system, even after extensive optimization. In a mammalian cell expression system, the Vγ9Vδ2 TCR was expressed in the form of a soluble heterodimer, which was suitable for crystal screening. Reduced-temperature cultivation (cold shock) increased the yield of the recombinant TCR. The recombinant purified TCR was used for crystal trials, and crystals that could be used for X-ray diffraction were obtained. Although we have not yet determined the crystal structure of the Vγ9Vδ2 TCR, we have established a procedure for Vγ9Vδ2 TCR expression and purification, which is useful for basic research and potentially for clinical application.
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Affiliation(s)
- Chaofei Cheng
- Stem Cell Research Center, Henan Key Laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- People's Hospital of Henan University, Zhengzhou, 450003, China
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China
| | - Zhendong Zhao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Centre for Tuberculosis Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
- Clinical Immunology Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.
| | - Guangzhi Liu
- Stem Cell Research Center, Henan Key Laboratory of Stem Cell Differentiation and Modification, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
- People's Hospital of Henan University, Zhengzhou, 450003, China.
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Basheer A, Jamal SB, Alzahrani B, Faheem M. Development of a tetravalent subunit vaccine against dengue virus through a vaccinomics approach. Front Immunol 2023; 14:1273838. [PMID: 38045699 PMCID: PMC10690774 DOI: 10.3389/fimmu.2023.1273838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023] Open
Abstract
Dengue virus infection (DVI) is a mosquito-borne disease that can lead to serious morbidity and mortality. Dengue fever (DF) is a major public health concern that affects approximately 3.9 billion people each year globally. However, there is no vaccine or drug available to deal with DVI. Dengue virus consists of four distinct serotypes (DENV1-4), each raising a different immunological response. In the present study, we designed a tetravalent subunit multi-epitope vaccine, targeting proteins including the structural protein envelope domain III (EDIII), precursor membrane proteins (prM), and a non-structural protein (NS1) from each serotype by employing an immunoinformatic approach. Only conserved sequences obtained through a multiple sequence alignment were used for epitope mapping to ensure efficacy against all serotypes. The epitopes were shortlisted based on an IC50 value <50, antigenicity, allergenicity, and a toxicity analysis. In the final vaccine construct, overall, 11 B-cell epitopes, 10 HTL epitopes, and 10 CTL epitopes from EDIII, prM, and NS1 proteins targeting all serotypes were selected and joined via KK, AAY, and GGGS linkers, respectively. We incorporated a 45-amino-acid-long B-defensins adjuvant in the final vaccine construct for a better immunogenic response. The vaccine construct has an antigenic score of 0.79 via VaxiJen and is non-toxic and non-allergenic. Our refined vaccine structure has a Ramachandran score of 96.4%. The vaccine has shown stable interaction with TLR3, which has been validated by 50 ns of molecular dynamics (MD) simulation. Our findings propose that a designed multi-epitope vaccine has substantial potential to elicit a strong immune response against all dengue serotypes without causing any adverse effects. Furthermore, the proposed vaccine can be experimentally validated as a probable vaccine, suggesting it may serve as an effective preventative measure against dengue virus infection.
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Affiliation(s)
- Amina Basheer
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Punjab, Pakistan
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Punjab, Pakistan
| | - Badr Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakakah, Saudi Arabia
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Punjab, Pakistan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States
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Kim HJ, Cha S, Choi JS, Lee JY, Kim KE, Kim JK, Kim J, Moon SY, Lee SHS, Park K, Won SY. scAAV2-Mediated Expression of Thioredoxin 2 and C3 Transferase Prevents Retinal Ganglion Cell Death and Lowers Intraocular Pressure in a Mouse Model of Glaucoma. Int J Mol Sci 2023; 24:16253. [PMID: 38003443 PMCID: PMC10671512 DOI: 10.3390/ijms242216253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Elevated intraocular pressure (IOP) in glaucoma causes retinal ganglion cell (RGC) loss and damage to the optic nerve. Although IOP is controlled pharmacologically, no treatment is available to restore retinal and optic nerve function. In this paper, we aimed to develop a novel gene therapy for glaucoma using an AAV2-based thioredoxin 2 (Trx2)-exoenzyme C3 transferase (C3) fusion protein expression vector (scAAV2-Trx2-C3). We evaluated the therapeutic effects of this vector in vitro and in vivo using dexamethasone (DEX)-induced glaucoma models. We found that scAAV2-Trx2-C3-treated HeLa cells had significantly reduced GTP-bound active RhoA and increased phosphor-cofilin Ser3 protein expression levels. scAAV2-Trx2-C3 was also shown to inhibit oxidative stress, fibronectin expression, and alpha-SMA expression in DEX-treated HeLa cells. NeuN immunostaining and TUNEL assay in mouse retinal tissues was performed to evaluate its neuroprotective effect upon RGCs, whereas changes in mouse IOP were monitored via rebound tonometer. The present study showed that scAAV2-Trx2-C3 can protect RGCs from degeneration and reduce IOP in a DEX-induced mouse model of glaucoma, while immunohistochemistry revealed that the expression of fibronectin and alpha-SMA was decreased after the transduction of scAAV2-Trx2-C3 in murine eye tissues. Our results suggest that AAV2-Trx2-C3 modulates the outflow resistance of the trabecular meshwork, protects retinal and other ocular tissues from oxidative damage, and may lead to the development of a gene therapeutic for glaucoma.
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Affiliation(s)
- Hee Jong Kim
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
| | - Seho Cha
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
| | - Jun-Sub Choi
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
| | - Joo Yong Lee
- Department of Ophthalmology, Asan Medical Center, College of Medicine, University of Ulsan, Seoul 05505, Republic of Korea; (J.Y.L.); (K.E.K.)
- Bio-Medical Institute of Technology, College of Medicine, University of Ulsan, Seoul 05505, Republic of Korea
| | - Ko Eun Kim
- Department of Ophthalmology, Asan Medical Center, College of Medicine, University of Ulsan, Seoul 05505, Republic of Korea; (J.Y.L.); (K.E.K.)
- Bio-Medical Institute of Technology, College of Medicine, University of Ulsan, Seoul 05505, Republic of Korea
| | - Jin Kwon Kim
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
| | - Jin Kim
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
| | - Seo Yun Moon
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
| | - Steven Hyun Seung Lee
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
| | - Keerang Park
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
| | - So-Yoon Won
- Institute of New Drug Development Research, Cdmogen Co., Ltd., Seoul 05855, Republic of Korea; (H.J.K.); (S.C.); (J.-S.C.); (J.K.K.); (J.K.); (S.Y.M.); (S.H.S.L.); (K.P.)
- Cdmogen Co., Ltd., Cheongju 28577, Republic of Korea
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Chung YH, Ortega-Rivera OA, Volckaert BA, Jung E, Zhao Z, Steinmetz NF. Viral nanoparticle vaccines against S100A9 reduce lung tumor seeding and metastasis. Proc Natl Acad Sci U S A 2023; 120:e2221859120. [PMID: 37844250 PMCID: PMC10614828 DOI: 10.1073/pnas.2221859120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/25/2023] [Indexed: 10/18/2023] Open
Abstract
Metastatic cancer accounts for 90% of all cancer-related deaths and continues to be one of the toughest challenges in cancer treatment. A growing body of data indicates that S100A9, a major regulator of inflammation, plays a central role in cancer progression and metastasis, particularly in the lungs, where S100A9 forms a premetastatic niche. Thus, we developed a vaccine against S100A9 derived from plant viruses and virus-like particles. Using multiple tumor mouse models, we demonstrate the effectiveness of the S100A9 vaccine candidates in preventing tumor seeding within the lungs and outgrowth of metastatic disease. The elicited antibodies showed high specificity toward S100A9 without cross-reactivity toward S100A8, another member of the S100A family. When tested in metastatic mouse models of breast cancer and melanoma, the vaccines significantly reduced lung tumor nodules after intravenous challenge or postsurgical removal of the primary tumor. Mechanistically, the vaccines reduce the levels of S100A9 within the lungs and sera, thereby increasing the expression of immunostimulatory cytokines with antitumor function [(interleukin) IL-12 and interferonγ] while reducing levels of immunosuppressive cytokines (IL-10 and transforming growth factorβ). This also correlated with decreased myeloid-derived suppressor cell populations within the lungs. This work has wide-ranging impact, as S100A9 is overexpressed in multiple cancers and linked with poor prognosis in cancer patients. The data presented lay the foundation for the development of therapies and vaccines targeting S100A9 to prevent metastasis.
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Affiliation(s)
- Young Hun Chung
- Department of Bioengineering, University of California, San Diego, CA92093
- Moores Cancer Center, University of California, San Diego, CA92093
| | | | | | - Eunkyeong Jung
- Department of NanoEngineering, University of California, San Diego, CA92093
| | - Zhongchao Zhao
- Moores Cancer Center, University of California, San Diego, CA92093
- Department of NanoEngineering, University of California, San Diego, CA92093
| | - Nicole F. Steinmetz
- Department of Bioengineering, University of California, San Diego, CA92093
- Moores Cancer Center, University of California, San Diego, CA92093
- Department of NanoEngineering, University of California, San Diego, CA92093
- Department of Radiology, University of California, San Diego, CA92093
- Institute for Materials Discovery and Design, University of California, San Diego, CA92093
- Center for Nano-ImmunoEngineering, University of California, San Diego, CA92093
- Center for Engineering in Cancer, University of California, San Diego, CA92093
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Pedron CN, Torres MDT, Oliveira CS, Silva AF, Andrade GP, Wang Y, Pinhal MAS, Cerchiaro G, da Silva Junior PI, da Silva FD, Radhakrishnan R, de la Fuente-Nunez C, Oliveira Junior VX. Molecular hybridization strategy for tuning bioactive peptide function. Commun Biol 2023; 6:1067. [PMID: 37857855 PMCID: PMC10587126 DOI: 10.1038/s42003-023-05254-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/17/2023] [Indexed: 10/21/2023] Open
Abstract
The physicochemical and structural properties of antimicrobial peptides (AMPs) determine their mechanism of action and biological function. However, the development of AMPs as therapeutic drugs has been traditionally limited by their toxicity for human cells. Tuning the physicochemical properties of such molecules may abolish toxicity and yield synthetic molecules displaying optimal safety profiles and enhanced antimicrobial activity. Here, natural peptides were modified to improve their activity by the hybridization of sequences from two different active peptide sequences. Hybrid AMPs (hAMPs) were generated by combining the amphipathic faces of the highly toxic peptide VmCT1, derived from scorpion venom, with parts of four other naturally occurring peptides having high antimicrobial activity and low toxicity against human cells. This strategy led to the design of seven synthetic bioactive variants, all of which preserved their structure and presented increased antimicrobial activity (3.1-128 μmol L-1). Five of the peptides (three being hAMPs) presented high antiplasmodial at 0.8 μmol L-1, and virtually no undesired toxic effects against red blood cells. In sum, we demonstrate that peptide hybridization is an effective strategy for redirecting biological activity to generate novel bioactive molecules with desired properties.
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Affiliation(s)
- Cibele Nicolaski Pedron
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Cyntia Silva Oliveira
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Adriana Farias Silva
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Gislaine Patricia Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Yiming Wang
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Giselle Cerchiaro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | | | - Fernanda Dias da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | - Ravi Radhakrishnan
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
| | - Vani Xavier Oliveira Junior
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil.
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Chauhan K, Mishra G, Kishore V, Kumar S. Appearance of de Gennes length in force-induced transitions. Phys Rev E 2023; 108:L042501. [PMID: 37978702 DOI: 10.1103/physreve.108.l042501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/12/2023] [Indexed: 11/19/2023]
Abstract
Using Langevin dynamic simulations, a simple coarse-grained model of a DNA protein construct is used to study the DNA rupture and the protein unfolding. We identify three distinct states: (i) zipped DNA and collapsed protein, (ii) unzipped DNA and stretched protein, and (iii) unzipped DNA and collapsed protein. Here, we find a phase diagram that shows these states depending on the size of the DNA handle and the protein. For a less stable protein, unfolding is solely governed by the size of the linker DNA, whereas if the protein's stability increases, complete unfolding becomes impossible because the rupture force for DNA has reached a saturation regime influenced by the de Gennes length. We show that unfolding occurs via a few intermediate states by monitoring the force-extension curve of the entire protein. We extend our study to a heterogeneous protein system, where similar intermediate states in two systems can lead to different protein unfolding paths.
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Affiliation(s)
- Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Garima Mishra
- Department of Physics, Ashoka University, Sonipat 131 029, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
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35
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Pajkos M, Erdős G, Dosztányi Z. The Origin of Discrepancies between Predictions and Annotations in Intrinsically Disordered Proteins. Biomolecules 2023; 13:1442. [PMID: 37892124 PMCID: PMC10604070 DOI: 10.3390/biom13101442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Disorder prediction methods that can discriminate between ordered and disordered regions have contributed fundamentally to our understanding of the properties and prevalence of intrinsically disordered proteins (IDPs) in proteomes as well as their functional roles. However, a recent large-scale assessment of the performance of these methods indicated that there is still room for further improvements, necessitating novel approaches to understand the strengths and weaknesses of individual methods. In this study, we compared two methods, IUPred and disorder prediction, based on the pLDDT scores derived from AlphaFold2 (AF2) models. We evaluated these methods using a dataset from the DisProt database, consisting of experimentally characterized disordered regions and subsets associated with diverse experimental methods and functions. IUPred and AF2 provided consistent predictions in 79% of cases for long disordered regions; however, for 15% of these cases, they both suggested order in disagreement with annotations. These discrepancies arose primarily due to weak experimental support, the presence of intermediate states, or context-dependent behavior, such as binding-induced transitions. Furthermore, AF2 tended to predict helical regions with high pLDDT scores within disordered segments, while IUPred had limitations in identifying linker regions. These results provide valuable insights into the inherent limitations and potential biases of disorder prediction methods.
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Affiliation(s)
| | | | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Stny 1/c, H-1117 Budapest, Hungary; (M.P.); (G.E.)
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Li H, Hou Z, Wang Y, Zhou Z, Cai J, Xin Q, Yin F, Li Z, Xu N. Methodology of stable peptide based on propargylated sulfonium. Biochem Biophys Rep 2023; 35:101508. [PMID: 37448811 PMCID: PMC10336417 DOI: 10.1016/j.bbrep.2023.101508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Peptides can be used as effective molecular tool for covalent modification of proteins and play important roles in ligand directed covalent modification. Tyr-selective protein modifications exert a profound impact on protein functionality. Here, we developed a general strategy that involves nucleophilic addition of alkyne for tyrosine modification. The terminal alkyne of propargyl sulfonium is motivated by the sulfonium center to react with phenolic hydroxyl. This approach provides a straightforward method for tyrosine modification due to its high yield in aqueous solution at physiological temperature. In addition, cyclic peptides could be obtained via adjusting pH to 8.0 from peptides consisting of tyrosine and methionine modified by propargyl bromide, and the resulting cyclic peptides are proved to have better stability, excellent 2-mercaptopyridine resistance and improved cellular uptakes. Furthermore, molecules made from the propargylated sulfonium have the potential to be used as warheads against tyrosine containing biomolecules. Collectively, we develop a direct and uncomplicated technique for modifying tyrosine residues, the strategy concerned can be widely utilized to construct stable peptides and biomolecules imaging.
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Affiliation(s)
- Heng Li
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhanfeng Hou
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Ziyuan Zhou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jin Cai
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Qilei Xin
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Naihan Xu
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
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37
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Zaroon, Yousaf N, Aslam S, Qureshi S, Bashir H. In silico investigation of a novel anti-EGFR scFv-IL-24 fusion protein induces apoptosis in malignant cells. J Mol Model 2023; 29:282. [PMID: 37606822 DOI: 10.1007/s00894-023-05690-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/11/2023] [Indexed: 08/23/2023]
Abstract
CONTEXT Epidermal growth factor receptor (EGFR), a member of the HER receptor family, is over expressed in various cancer cells. Using tumor-specific antibodies to deliver cytotoxic agents directly to the tumor cells is an effective treatment strategy. Targeted therapy by fusing anti-EGFR scFv with tumor-specific cytokines promises the emergence of a new era. METHODS We designed a novel immuno-apoptotic fusion protein, anti-EGFR scFv-IL-24, consisting of a specific cancer cell targeting antibody and recombinant cytokine IL-24 to explore its anti-cancerous potential. Amino acid sequences of both anti-EGFR scFv and IL-24 were fused using a specific rigid linker. In silico characterization of the designed fusion protein like to predict the primary, secondary, physiochemical properties, quality, and structural validation using online bioinformatic tools. The newly designed fusion protein consists of 402 amino acids that showed good quality with a predicted value of 76.7% having 81.5% residues in the most favored region as predicted by ERRAT2 and Ramachandran plot analysis. Docking and simulation studies were performed using HDOCK and Desmond module of Schrodinger. All the parameters of quality, validity, interaction analysis, and stability suggested that the fused molecule is fully operational and functional. The results of the study support that the anti-EGFR scFv-IL-24 fused protein could be proved as a novel candidate to combat cancer.
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Affiliation(s)
- Zaroon
- Centre for Applied Molecular Biology, University of the Punjab, 87-West Canal, Bank Road, Lahore, 53700, Pakistan
| | - Numan Yousaf
- Department of Bioscience, COMSAT University Islamabad, Islamabad, Pakistan
| | - Shakira Aslam
- Centre for Applied Molecular Biology, University of the Punjab, 87-West Canal, Bank Road, Lahore, 53700, Pakistan
| | - Shahnila Qureshi
- Centre for Applied Molecular Biology, University of the Punjab, 87-West Canal, Bank Road, Lahore, 53700, Pakistan
| | - Hamid Bashir
- Centre for Applied Molecular Biology, University of the Punjab, 87-West Canal, Bank Road, Lahore, 53700, Pakistan.
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38
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Wei H, Wang H, Wang G, Qu L, Jiang L, Dai S, Chen X, Zhang Y, Chen Z, Li Y, Guo M, Chen Y. Structures of p53/BCL-2 complex suggest a mechanism for p53 to antagonize BCL-2 activity. Nat Commun 2023; 14:4300. [PMID: 37463921 DOI: 10.1038/s41467-023-40087-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Mitochondrial apoptosis is strictly controlled by BCL-2 family proteins through a subtle network of protein interactions. The tumor suppressor protein p53 triggers transcription-independent apoptosis through direct interactions with BCL-2 family proteins, but the molecular mechanism is not well understood. In this study, we present three crystal structures of p53-DBD in complex with the anti-apoptotic protein BCL-2 at resolutions of 2.3-2.7 Å. The structures show that two loops of p53-DBD penetrate directly into the BH3-binding pocket of BCL-2. Structure-based mutations at the interface impair the p53/BCL-2 interaction. Specifically, the binding sites for p53 and the pro-apoptotic protein Bax in the BCL-2 pocket are mostly identical. In addition, formation of the p53/BCL-2 complex is negatively correlated with the formation of BCL-2 complexes with pro-apoptotic BCL-2 family members. Defects in the p53/BCL-2 interaction attenuate p53-mediated cell apoptosis. Overall, our study provides a structural basis for the interaction between p53 and BCL-2, and suggests a molecular mechanism by which p53 regulates transcription-independent apoptosis by antagonizing the interaction of BCL-2 with pro-apoptotic BCL-2 family members.
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Affiliation(s)
- Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Genxin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Lingzhi Qu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Longying Jiang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ye Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Youjun Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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Nawrocka D, Krzyscik MA, Sluzalska KD, Otlewski J. Dual-Warhead Conjugate Based on Fibroblast Growth Factor 2 Dimer Loaded with α-Amanitin and Monomethyl Auristatin E Exhibits Superior Cytotoxicity towards Cancer Cells Overproducing Fibroblast Growth Factor Receptor 1. Int J Mol Sci 2023; 24:10143. [PMID: 37373291 DOI: 10.3390/ijms241210143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Targeting fibroblast growth factor receptor 1 (FGFR1) is a promising therapeutic strategy for various cancers associated with alterations in the FGFR1 gene. In this study, we developed a highly cytotoxic bioconjugate based on fibroblast growth factor 2 (FGF2), which is a natural ligand of this receptor, and two potent cytotoxic drugs-α-amanitin and monomethyl auristatin E-with completely independent mechanistic modes of action. Utilizing recombinant DNA technology, we produced an FGF2 N- to C-end dimer that exhibited superior internalization capacity in FGFR1-positive cells. The drugs were site-specifically attached to the targeting protein using SnoopLigase- and evolved sortase A-mediated ligations. The resulting dimeric dual-warhead conjugate selectively binds to the FGFR1 and utilizes receptor-mediated endocytosis to enter the cells. Moreover, our results demonstrate that the developed conjugate exhibits about 10-fold higher cytotoxic potency against FGFR1-positive cell lines than an equimolar mixture of single-warhead conjugates. The diversified mode of action of the dual-warhead conjugate may help to overcome the potential acquired resistance of FGFR1-overproducing cancer cells to single cytotoxic drugs.
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Affiliation(s)
- Daria Nawrocka
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Mateusz Adam Krzyscik
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Katarzyna Dominika Sluzalska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Jacek Otlewski
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
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40
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Wittenborn EC, Thomas WC, Houghton KA, Wirachman ES, Wu Y, Marletta MA. Role of the Coiled-Coil Domain in Allosteric Activity Regulation in Soluble Guanylate Cyclase. Biochemistry 2023; 62:1568-1576. [PMID: 37129924 PMCID: PMC10686098 DOI: 10.1021/acs.biochem.3c00052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Soluble guanylate cyclase (sGC) is the primary nitric oxide (NO) receptor in higher eukaryotes, including humans. NO-dependent signaling via sGC is associated with important physiological effects in the vascular, pulmonary, and neurological systems, and sGC itself is an established drug target for the treatment of pulmonary hypertension due to its central role in vasodilation. Despite isolation in the late 1970s, high-resolution structural information on full-length sGC remained elusive until recent cryo-electron microscopy structures were determined of the protein in both the basal unactivated state and the NO-activated state. These structures revealed large-scale conformational changes upon activation that appear to be centered on rearrangements within the coiled-coil (CC) domains in the enzyme. Here, a structure-guided approach was used to engineer constitutively unactivated and constitutively activated sGC variants through mutagenesis of the CC domains. These results demonstrate that the activation-induced conformational change in the CC domains is necessary and sufficient for determining the level of sGC activity.
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Affiliation(s)
- Elizabeth C. Wittenborn
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - William C. Thomas
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kimberly A. Houghton
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Erika S. Wirachman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yang Wu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael A. Marletta
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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41
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Choyam S, Kammara R. Understanding the Necessity of Regulatory Protein Machinery in Heterologous Expression of Class-III Type of Ocins. Protein J 2023:10.1007/s10930-023-10106-8. [PMID: 36976382 DOI: 10.1007/s10930-023-10106-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
Abstract
To date, there have been no or just a few reports of successful cloning and expression to create biologically active ocins or bacteriocins. Cloning, expression, and production of class I ocins are problematic because of their structural arrangements, coordinated functions, size, and posttranslational modifications. Mass synthesis of these molecules is necessary for commercialization and to restrict the excessive use of conventional antibiotics, which encourages the development of antibiotic-resistant bacteria. In the case of class III ocins, there are no reports of obtaining biological active proteins to date. Being able to obtain biologically active proteins requires an understanding of mechanistic features due to their expanding importance and broad spectrum of activity. As a result, we intend to clone and express the class III type. The class I types that are devoid of posttranslational modifications were transformed into class III through fusion. Therefore, this construct resembles a class III type ocin. With the exception of Zoocin, expression of the proteins was found to be physiologically ineffective after cloning. But, few cell morphological changes such as elongation, aggregation, and the formation of terminal hyphae were observed. However, it was discovered that the target indicator had been altered to Vibrio spp. in a few. All the three ocins were subjected to in-silico structure prediction/analysis. Finally, we confirm the existence of unidentified additional intrinsic factors for successful expression to obtain biologically active protein.
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Affiliation(s)
- Shilja Choyam
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, Mysore, India
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42
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Wang Z, Mei L, Guo C, Huang S, Shi WQ, Li X, Feng W, Li X, Yang C, Yuan L. Supramolecular Shish Kebabs: Higher Order Dimeric Structures from Ring-in-Rings Complexes with Conformational Adaptivity. Angew Chem Int Ed Engl 2023; 62:e202216690. [PMID: 36652350 DOI: 10.1002/anie.202216690] [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: 11/14/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
Use of abiotic chemical systems for understanding higher order superstructures is challenging. Here we report a ring-in-ring(s) system comprising a hydrogen-bonded macrocycle and cyclobis(paraquat-o-phenylene) tetracation (o-Box) or cyclobis(paraquat-p-phenylene) tetracation (CBPQT4+ , p-Box) that assembles to construct discrete higher order structures with adaptive conformation. As indicated by mass spectrometry, computational modeling, NMR spectroscopy, and single-crystal X-ray diffraction analysis, this ring-in-ring(s) system features the box-directed aggregation of multiple macrocycles, leading to generation of several stable species such as H4G (1 a/o-Box) and H5G (1 a/o-Box). Remarkably, a dimeric shish-kebab-like ring-in-rings superstructure H7G2 (1 a/o-Box) or H8G2 (1 a/p-Box) is formed from the coaxial stacking of two ring-in-rings units. The formation of such unique dimeric superstructures is attributed to the large π-surface of this 2D planar macrocycle and the conformational variation of both host and guest.
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Affiliation(s)
- Zhenwen Wang
- College of Chemistry, Key Laboratory of Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu, Sichuan, 610064, China) (The first email address should be
| | - Lei Mei
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenxing Guo
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, China
| | - Song Huang
- College of Chemistry, Key Laboratory of Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu, Sichuan, 610064, China) (The first email address should be
| | - Wei-Qun Shi
- Laboratory of Nuclear Energy Chemistry, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Li
- College of Chemistry, Key Laboratory of Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu, Sichuan, 610064, China) (The first email address should be
| | - Wen Feng
- College of Chemistry, Key Laboratory of Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu, Sichuan, 610064, China) (The first email address should be
| | - Xiaopeng Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518071, China.,University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Cheng Yang
- College of Chemistry, Key Laboratory of Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu, Sichuan, 610064, China) (The first email address should be
| | - Lihua Yuan
- College of Chemistry, Key Laboratory of Radiation Physics and Technology of Ministry of Education, Sichuan University, Chengdu, Sichuan, 610064, China) (The first email address should be
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Seifi R, Ayat H, Ahadi AM. Design and construction of a chimeric peptide, MeICT/IMe-AGAP, from two anti-cancer toxins of Iranian Mesobuthus eupeus scorpion. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2023; 12:27-36. [PMID: 37201031 PMCID: PMC10186859 DOI: 10.22099/mbrc.2023.46450.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Scorpion venom contains various toxin peptides with pharmacological and biological properties. Scorpion toxins specifically interact with membrane ion channels which play key roles in progression of cancer. Therefore, scorpion toxins have received special attention for targeting cancer cells. Two new toxins MeICT and IMe-AGAP, isolated from Iranian yellow scorpion, Mesobuthus eupeus, interact specifically with chloride and sodium channels, respectively. Anti-cancer properties of MeICT and IMe-AGAP have been determined before, in addition they show 81 and 93% similarity with two well-known anti-cancer toxins, CTX and AGAP, respectively. The aim of this study was construction of a fusion peptide MeICT/IMe-AGAP to target different ion channels involved in cancer progression. Design and structure of the fusion peptide were investigated by bioinformatics studies. Two fragments encoding MeICT and IMe-AGAP were fused using overlapping primers by SOEing-PCR. MeICT/IMe-AGAP chimeric fragment was cloned into pET32Rh vector, expressed in Escherichia coli host and analyzed by SDS-PAGE. The in silico studies showed that chimeric peptide with GPSPG linker preserved the three-dimensional structure of both peptides and can be functional. Due to the high expression of chloride and sodium channels in various cancer cells, MeICT/IMe-AGAP fusion peptide can be used as an effective agent to target both channels in cancers, simultaneously.
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Affiliation(s)
| | - Hoda Ayat
- Corresponding Author: Department of Genetics, Shahrekord University, Rahbar Shahrekord, Iran. Tel: +98 38 32324401; Fax: +98 38 32324402; E.mail: And
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Huang C, Huang J, Zhu S, Tang T, Chen Y, Qian F. Multivalent nanobodies with rationally optimized linker and valency for intravitreal VEGF neutralization. Chem Eng Sci 2023. [DOI: 10.1016/j.ces.2023.118521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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45
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Vugmeyster L, Nichols PJ, Ostrovsky D, McKnight CJ, Vögeli B. Slow methyl axes motions in perdeuterated villin headpiece subdomain probed by cross-correlated NMR relaxation measurements. MAGNETOCHEMISTRY (BASEL, SWITZERLAND) 2023; 9:33. [PMID: 36776538 PMCID: PMC9910280 DOI: 10.3390/magnetochemistry9010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Protein methyl groups can participate in multiple motional modes on different time scales. Sub-nanosecond to nano-second time scale motions of methyl axes are particularly challenging to detect for small proteins in solutions. In this work we employ NMR relaxation interference between the methyl H-H/H-C dipole-dipole interactions [Sun&Tugarinov, J. Magn. Reason. 2012] to characterize methyl axes motions as a function of temperature in a small model protein villin headpiece subdomain (HP36), in which all non-exchangeable protons are deuterated with the exception of methyl groups of leucine and valine residues. The data points to the existence of slow motional modes of methyl axes on sub-nanosecond to nanosecond time scales. Further, at high temperatures for which the overall tumbling of the protein is on the order of 2 ns, we observe a coupling between the slow internal motion and the overall molecular tumbling, based on the anomalous order parameters and their temperature-dependent trends. The addition of 28%(w/w) glycerol-d8 increases the viscosity of the solvent and separates the timescales of internal and overall tumbling, thus permitting for another view of the necessity of the coupling assumption for these sites at high temperatures.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, CO 80204
| | - Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado at Denver, Denver, CO 80204
| | - C. James McKnight
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, 02118
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045
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Lintott LG, Nutter LMJ. Genetic and Molecular Quality Control of Genetically Engineered Mice. Methods Mol Biol 2023; 2631:53-101. [PMID: 36995664 DOI: 10.1007/978-1-0716-2990-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Genetically engineered mice are used as avatars to understand mammalian gene function and develop therapies for human disease. During genetic modification, unintended changes can occur, and these changes may result in misassigned gene-phenotype relationships leading to incorrect or incomplete experimental interpretations. The types of unintended changes that may occur depend on the allele type being made and the genetic engineering approach used. Here we broadly categorize allele types as deletions, insertions, base changes, and transgenes derived from engineered embryonic stem (ES) cells or edited mouse embryos. However, the methods we describe can be adapted to other allele types and engineering strategies. We describe the sources and consequ ences of common unintended changes and best practices for detecting both intended and unintended changes by screening and genetic and molecular quality control (QC) of chimeras, founders, and their progeny. Employing these practices, along with careful allele design and good colony management, will increase the chance that investigations using genetically engineered mice will produce high-quality reproducible results, to enable a robust understanding of gene function, human disease etiology, and therapeutic development.
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Affiliation(s)
- Lauri G Lintott
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada.
- The Hospital for Sick Children, Toronto, ON, Canada.
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Li P, Wang X, Zhang C, Xu D. Processive binding mechanism of Cel9G from Clostridium cellulovorans: molecular dynamics and free energy landscape investigations. Phys Chem Chem Phys 2023; 25:646-657. [DOI: 10.1039/d2cp04830b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The processive binding mechanism of cellulose by Cel9G from C. cellulovorans was investigated by MD and metadynamics simulations.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Chunchun Zhang
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
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Chathuranga WAG, Hewawaduge C, Nethmini NAN, Kim TH, Kim JH, Ahn YH, Yoon IJ, Yoo SS, Park JH, Lee JS. Efficacy of a Novel Multiepitope Vaccine Candidate against Foot-and-Mouth Disease Virus Serotype O and A. Vaccines (Basel) 2022; 10:vaccines10122181. [PMID: 36560591 PMCID: PMC9786174 DOI: 10.3390/vaccines10122181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious and economically devastating disease in cloven-hoofed animals. To prevent the spread of FMD virus (FMDV), traditional inactivated vaccines are used to immunize susceptible animals in disease-endemic countries. However, the inactivated FMD vaccine has several limitations, including safety concerns. To overcome these limitations, subunit proteins have been studied as alternative vaccine candidates. In this study, we designed two multiepitope recombinant proteins (OVM and AVM) containing antigenic sites (residue of VP1 132-162 and residue of VP1 192-212) of three topotypes of FMDV serotype O or three topotypes of FMDV serotype A. Each recombinant protein was efficiently expressed in Escherichia coli with high solubility, and the immunogenicity and protective efficacy of the proteins as FMD vaccine candidates were evaluated. The results showed that OVM and AVM emulsified with ISA201 adjuvant induced effective antigen-specific humoral and cell-mediated immune responses and successfully protected mice from O/Jincheon/SKR/2014, O/VET/2013, and A/Malaysia/97 viruses. In addition, intramuscular immunization of pigs with the OVM and AVM emulsified with ISA201 elicited effective levels of neutralizing antibodies to the viruses with homologous epitopes. Importantly, OVM-AVM emulsified with CAvant®SOE-X adjuvant conferred 100% protection against the O/Jincheon/SKR/2014 virus with homologous residues and 75% protection against A/SKR/GP/2018 with heterologous residues. The results presented in this study suggest that the combination of OVM and AVM protein with an effective adjuvant could yield an effective and safe vaccine candidate for the prevention and control of foot-and-mouth disease. In addition, our results provide a vaccine platform that can safely, cost-efficiently, and rapidly generate protective vaccine candidates against diverse FMDVs.
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Affiliation(s)
- W. A. Gayan Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Chamith Hewawaduge
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - N. A. Nadeeka Nethmini
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Tae-Hwan Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Ju Hun Kim
- Komipharm International Co., Ltd., Siheung 15094, Gyeonggi-do, Republic of Korea
| | - Young-Hoon Ahn
- Choong Ang Vaccine Laboratory Co., Ltd., Daejeon 34055, Republic of Korea
| | - In-Joong Yoon
- Choong Ang Vaccine Laboratory Co., Ltd., Daejeon 34055, Republic of Korea
| | - Sung-Sik Yoo
- Choong Ang Vaccine Laboratory Co., Ltd., Daejeon 34055, Republic of Korea
| | - Jong-Hyeon Park
- Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea
- Correspondence: (J.-H.P.); (J.-S.L.); Tel.: +82-31-467-1719 (J.-H.P.); +82-42-821-6753 (J.-S.L.)
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
- Correspondence: (J.-H.P.); (J.-S.L.); Tel.: +82-31-467-1719 (J.-H.P.); +82-42-821-6753 (J.-S.L.)
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Bragagnolo N, Audette GF. Solution characterization of the dynamic conjugative entry exclusion protein TraG. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:064702. [PMID: 36590369 PMCID: PMC9797247 DOI: 10.1063/4.0000171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through a process termed entry exclusion. In the donor cell, it interacts with TraN to facilitate mating pair stabilization; however, if a mating pore forms between bacteria with identical plasmids, TraG* interacts with its cognate TraS in the inner membrane of the recipient bacterium to prevent redundant donor-donor conjugation. Structural studies of TraG* from the R100 plasmid have revealed the presence of a dynamic region between the N- and C-terminal domains of TraG. Thermofluor, circular dichroism, collision-induced unfolding-mass spectrometry, and size exclusion chromatography linked to multiangle light scattering and small angle x-ray scattering experiments indicated an N-terminal truncation mutant displayed higher stability and less disordered content relative to full-length TraG*. The 45 N-terminal residues of TraG* are hypothesized to serve as part of a flexible linker between the two independently functioning domains.
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Affiliation(s)
- Nicholas Bragagnolo
- Centre for Research on Biomolecular Interactions, Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Gerald F. Audette
- Centre for Research on Biomolecular Interactions, Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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Lin Z, Jing Y, Huang Y, Yang S, Chen S, Ou Y, Pistolozzi M, Yang X. A cleavable self-aggregating tag scheme for the expression and purification of disulfide bonded proteins and peptides. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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