1
|
Aram C, Alijanizadeh P, Saleki K, Karami L. Development of an ancestral DC and TLR4-inducing multi-epitope peptide vaccine against the spike protein of SARS-CoV and SARS-CoV-2 using the advanced immunoinformatics approaches. Biochem Biophys Rep 2024; 39:101745. [PMID: 38974021 PMCID: PMC11225186 DOI: 10.1016/j.bbrep.2024.101745] [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: 03/12/2024] [Revised: 04/26/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024] Open
Abstract
The oldest human coronavirus that started pandemics is severe acute respiratory syndrome virus (SARS-CoV). While SARS-CoV was eradicated, its new version, SARS-CoV2, caused the global pandemic of COVID-19. Evidence highlights the harmful events orchestrated by these viruses are mediated by Spike (S)P protein. Experimental epitopes of the S protein which were overlapping and ancestral between SARS-CoV and SARS-CoV-2 were obtained from the immune epitopes database (IEDB). The epitopes were then assembled in combination with a 50 S ribosomal protein L7/L12 adjuvant, a Mycobacterium tuberculosis-derived element and mediator of dendritic cells (DCs) and toll-like receptor 4 (TLR4). The immunogenic sequence was modeled by the GalaxyWeb server. After the improvement and validation of the protein structure, the physico-chemical properties and immune simulation were performed. To investigate the interaction with TLR3/4, Molecular Dynamics Simulation (MDS) was used. By merging the 17 B- and T-lymphocyte (HTL/CTL) epitopes, the vaccine sequence was created. Also, the Ramachandran plot presented that most of the residues were located in the most favorable and allowed areas. Moreover, SnapGene was successful in cloning the DNA sequence linked to our vaccine in the intended plasmid. A sequence was inserted between the XhoI and SacI position of the pET-28a (+) vector, and simulating the agarose gel revealed the existence of the inserted gene in the cloned plasmid with SARS vaccine (SARSV) construct, which has a 6565 bp in length overall. In terms of cytokines/IgG response, immunological simulation revealed a strong immune response. The stabilized vaccine showed strong interactions with TLR3/4, according to Molecular Dynamics Simulation (MDS) analysis. The present ancestral vaccine targets common sequences which seem to be valuable targets even for the new variant SARS-CoV-2.
Collapse
Affiliation(s)
- Cena Aram
- Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Parsa Alijanizadeh
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Kiarash Saleki
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Leila Karami
- Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| |
Collapse
|
2
|
Masum MHU, Wajed S, Hossain MI, Moumi NR, Talukder A, Rahman MM. An mRNA vaccine for pancreatic cancer designed by applying in silico immunoinformatics and reverse vaccinology approaches. PLoS One 2024; 19:e0305413. [PMID: 38976715 PMCID: PMC11230540 DOI: 10.1371/journal.pone.0305413] [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: 03/16/2024] [Accepted: 05/30/2024] [Indexed: 07/10/2024] Open
Abstract
Pancreatic ductal adenocarcinoma is the most prevalent pancreatic cancer, which is considered a significant global health concern. Chemotherapy and surgery are the mainstays of current pancreatic cancer treatments; however, a few cases are suitable for surgery, and most of the cases will experience recurrent episodes. Compared to DNA or peptide vaccines, mRNA vaccines for pancreatic cancer have more promise because of their delivery, enhanced immune responses, and lower proneness to mutation. We constructed an mRNA vaccine by analyzing S100 family proteins, which are all major activators of receptors for advanced glycation end products. We applied immunoinformatic approaches, including physicochemical properties analysis, structural prediction and validation, molecular docking study, in silico cloning, and immune simulations. The designed mRNA vaccine was estimated to have a molecular weight of 165023.50 Da and was highly soluble (grand average of hydropathicity of -0.440). In the structural assessment, the vaccine seemed to be a well-stable and functioning protein (Z score of -8.94). Also, the docking analysis suggested that the vaccine had a high affinity for TLR-2 and TLR-4 receptors. Additionally, the molecular mechanics with generalized Born and surface area solvation analysis of the "Vaccine-TLR-2" (-141.07 kcal/mol) and "Vaccine-TLR-4" (-271.72 kcal/mol) complexes also suggests a strong binding affinity for the receptors. Codon optimization also provided a high expression level with a GC content of 47.04% and a codon adaptation index score 1.0. The appearance of memory B-cells and T-cells was also observed over a while, with an increased level of helper T-cells and immunoglobulins (IgM and IgG). Moreover, the minimum free energy of the mRNA vaccine was predicted at -1760.00 kcal/mol, indicating the stability of the vaccine following its entry, transcription, and expression. This hypothetical vaccine offers a groundbreaking tool for future research and therapeutic development of pancreatic cancer.
Collapse
Affiliation(s)
- Md Habib Ullah Masum
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Shah Wajed
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
- Infectiology: Biology of Infectious Diseases, Universite Paris-Saclay, Gif-sur-Yvette, France
| | - Md Imam Hossain
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Nusrat Rahman Moumi
- Medical Sciences, University of Central Lancashire, Preston, Lancashire, United Kingdom
| | - Asma Talukder
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
- School of Pharmacy and Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Brisbane, Queensland, Australia
| | - Md Mijanur Rahman
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
- School of Pharmacy and Medical Sciences, and Menzies Health Institute Queensland, Griffith University, Brisbane, Queensland, Australia
| |
Collapse
|
3
|
Roy A, Swetha RG, Basu S, Biswas R, Ramaiah S, Anbarasu A. Integrating pan-genome and reverse vaccinology to design multi-epitope vaccine against Herpes simplex virus type-1. 3 Biotech 2024; 14:176. [PMID: 38855144 PMCID: PMC11153438 DOI: 10.1007/s13205-024-04022-6] [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: 03/08/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Herpes simplex virus type-1 (HSV-1), the etiological agent of sporadic encephalitis and recurring oral (sometimes genital) infections in humans, affects millions each year. The evolving viral genome reduces susceptibility to existing antivirals and, thus, necessitates new therapeutic strategies. Immunoinformatics strategies have shown promise in designing novel vaccine candidates in the absence of a clinically licensed vaccine to prevent HSV-1. However, to encourage clinical translation, the HSV-1 pan-genome was integrated with the reverse-vaccinology pipeline for rigorous screening of universal vaccine candidates. Viral targets were screened from 104 available complete genomes. Among 364 proteins, envelope glycoprotein D being an outer membrane protein with a high antigenicity score (> 0.4) and solubility (> 0.6) was selected for epitope screening. A total of 17 T-cell and 4 B-cell epitopes with highly antigenic, immunogenic, non-toxic properties and high global population coverage were identified. Furthermore, 8 vaccine constructs were designed using different combinations of epitopes and suitable linkers. VC-8 was identified as the most potential vaccine candidate regarding chemical and structural stability. Molecular docking revealed high interactive affinity (low binding energy: - 56.25 kcal/mol) of VC-8 with the target elicited by firm intermolecular H-bonds, salt-bridges, and hydrophobic interactions, which was validated with simulations. Compatibility of the vaccine candidate to be expressed in pET-29(a) + plasmid was established by in silico cloning studies. Immune simulations confirmed the potential of VC-8 to trigger robust B-cell, T-cell, cytokine, and antibody-mediated responses, thereby suggesting a promising candidate for the future of HSV-1 prevention. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04022-6.
Collapse
Affiliation(s)
- Aditi Roy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Rayapadi G. Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Soumya Basu
- Department of Biotechnology, NIST University, Berhampur, Odisha 761008 India
| | - Rhitam Biswas
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| |
Collapse
|
4
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Exploring conformational landscapes and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variant complexes with the ACE2 receptor using AlphaFold2-based structural ensembles and molecular dynamics simulations. Phys Chem Chem Phys 2024; 26:17720-17744. [PMID: 38869513 DOI: 10.1039/d4cp01372g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In this study, we combined AlphaFold-based approaches for atomistic modeling of multiple protein states and microsecond molecular simulations to accurately characterize conformational ensembles evolution and binding mechanisms of convergent evolution for the SARS-CoV-2 spike Omicron variants BA.1, BA.2, BA.2.75, BA.3, BA.4/BA.5 and BQ.1.1. We employed and validated several different adaptations of the AlphaFold methodology for modeling of conformational ensembles including the introduced randomized full sequence scanning for manipulation of sequence variations to systematically explore conformational dynamics of Omicron spike protein complexes with the ACE2 receptor. Microsecond atomistic molecular dynamics (MD) simulations provide a detailed characterization of the conformational landscapes and thermodynamic stability of the Omicron variant complexes. By integrating the predictions of conformational ensembles from different AlphaFold adaptations and applying statistical confidence metrics we can expand characterization of the conformational ensembles and identify functional protein conformations that determine the equilibrium dynamics for the Omicron spike complexes with the ACE2. Conformational ensembles of the Omicron RBD-ACE2 complexes obtained using AlphaFold-based approaches for modeling protein states and MD simulations are employed for accurate comparative prediction of the binding energetics revealing an excellent agreement with the experimental data. In particular, the results demonstrated that AlphaFold-generated extended conformational ensembles can produce accurate binding energies for the Omicron RBD-ACE2 complexes. The results of this study suggested complementarities and potential synergies between AlphaFold predictions of protein conformational ensembles and MD simulations showing that integrating information from both methods can potentially yield a more adequate characterization of the conformational landscapes for the Omicron RBD-ACE2 complexes. This study provides insights in the interplay between conformational dynamics and binding, showing that evolution of Omicron variants through acquisition of convergent mutational sites may leverage conformational adaptability and dynamic couplings between key binding energy hotspots to optimize ACE2 binding affinity and enable immune evasion.
Collapse
Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Chaudhuri D, Majumder S, Datta J, Giri K. Repurposing of therapeutic antibodies against dengue virus envelope protein receptor binding domain. Arch Microbiol 2024; 206:312. [PMID: 38900285 DOI: 10.1007/s00203-024-04039-8] [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: 05/06/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/21/2024]
Abstract
Dengue virus (DENV) is the leading cause of numerous deaths every year due to its high infectivity. In this study we have tried to target the DENV envelope protein receptor binding domain, the region crucial for binding to host receptors which leads to membrane fusion and entry of the viral genome into the human host cell. We have taken 13 known FDA approved antiviral therapeutic antibodies from therapeutic antibody database and tried to repurpose them against the DENV envelope protein. Based on the humanness analysis, 10 antibodies were selected against the DENV envelope protein. Computational affinity maturation of the 10 selected antibodies was performed to increase their binding affinity and specificity against the DENV envelope protein which ultimately led to 8 mutant antibodies having better binding affinity than the native ones. Molecular Dynamics (MD) simulation shows that, the stability of the complexes involving both the native and mutant antibodies were found to be the same although the binding energy between the protein and the respective antibodies was seen to improve upon computational affinity maturation. Contact analyses show similar robustness of the interaction for both the mutant and native antibodies during complex formation with the DENV envelope protein. This has led to the selection of total 18 antibodies including 10 natural and 8 affinity matured mutants which have a high probability of interacting with the DENV envelope protein. Finally, based on all these analyses along with heated MD simulation, Bamlanivimab, Etesivimab and Tixagevimab with a mutation of residue 100 of the heavy chain from serine to tyrosine were selected as prospective therapeutic antibodies to combat DENV infection. This study may open a new avenue in designing therapeutics to combat Dengue viral infection.
Collapse
Affiliation(s)
- Dwaipayan Chaudhuri
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Satyabrata Majumder
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Joyeeta Datta
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Kalyan Giri
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India.
| |
Collapse
|
7
|
Satheesh S, Al Solami L. Antifouling activities of proteinase K and α-amylase enzymes: Laboratory bioassays and in silico analysis. Heliyon 2024; 10:e31683. [PMID: 38828329 PMCID: PMC11140711 DOI: 10.1016/j.heliyon.2024.e31683] [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: 01/22/2024] [Revised: 05/02/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
The application of enzymes as antifoulants is one of the environment-friendly strategies in biofouling management. In this study, antifouling activities of commercially available proteinase K and α-amylase enzymes were evaluated using barnacle larva and biofilm-forming bacteria as test organisms. The enzymes were also tested against barnacle cement protein through in silico analysis. The results showed that both enzymes inhibited the attachment of bacteria and settlement of barnacle larvae on the test surface. The lowest minimum inhibitory concentration of 0.312 mg ml-1 was exhibited by proteinase K against biofilm-forming bacteria. The calculated LC50 values for proteinase K and α-amylase against the barnacle nauplii were 91.8 and 230.96 mg ml-1 respectively. While α-amylase showed higher antibiofilm activity, proteinase K exhibited higher anti-larval settlement activity. Similarly, in silico analysis of the enzymes revealed promising anti-settlement activity, as the enzymes showed good binding scores with barnacle cement protein. Overall, the results suggested that the enzymes proteinase K and α-amylase could be used in antifouling coatings to reduce the settlement of biofouling on artificial materials in the marine environment.
Collapse
Affiliation(s)
- Sathianeson Satheesh
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Lafi Al Solami
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
8
|
Araujo-Abad S, Rizzuti B, Soto-Conde L, Vidal M, Abian O, Velazquez-Campoy A, Neira JL, de Juan Romero C. Citrullinating enzyme PADI4 and transcriptional repressor RING1B bind in cancer cells. Int J Biol Macromol 2024; 274:133163. [PMID: 38878927 DOI: 10.1016/j.ijbiomac.2024.133163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/26/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
Polycomb groups (PcGs) are transcriptional repressors, formed by a complex of several proteins, involved in multicellular development and cancer epigenetics. One of these proteins is the E3 ubiquitin-protein ligase RING1 (or RING1B), associated with the regulation of transcriptional repression and responsible for monoubiquitylation of the histone H2A. On the other hand, PADI4 is one of the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline, and it is also involved in the development of glioblastoma, among other types of cancers. In this work, we showed the association of PADI4 and RING1B in the nucleus and cytosol in several cancer cell lines by using immunofluorescence and proximity ligation assays. Furthermore, we demonstrated that binding was hampered in the presence of GSK484, an enzymatic PADI4 inhibitor, suggesting that RING1B could bind to the active site of PADI4, as confirmed by protein-protein docking simulations. In vitro and in silico findings showed that binding to PADI4 occurred for the isolated fragments corresponding to both the N-terminal (residues 1-221) and C-terminal (residues 228-336) regions of RING1B. Binding to PADI4 was also hampered by GSK484, as shown by isothermal titration calorimetry (ITC) experiments for the sole N-terminal region, and by both NMR and ITC for the C-terminal one. The dissociation constants between PADI4 and any of the two isolated RING1B fragments were in the low micromolar range (~2-10 μM), as measured by fluorescence and ITC. The interaction between RING1B and PADI4 might imply citrullination of the former, leading to several biological consequences, as well as being of potential therapeutic relevance for improving cancer treatment with the generation of new antigens.
Collapse
Affiliation(s)
- Salome Araujo-Abad
- Cancer Research Group, Faculty of Engineering and Applied Sciences, Universidad de Las Américas, 170124 Quito, Ecuador; IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain.
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy; Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | | | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, 03203 Elche (Alicante), Spain.
| |
Collapse
|
9
|
Miranda-Roblero HO, Saavedra-Salazar LF, Galicia-Moreno M, Arceo-Orozco S, Caloca-Camarena F, Sandoval-Rodriguez A, García-Bañuelos J, Frias-Gonzalez C, Almeida-López M, Martínez-López E, Armendariz-Borunda J, Monroy-Ramirez HC. Pirfenidone Reverts Global DNA Hypomethylation, Promoting DNMT1/UHRF/PCNA Coupling Complex in Experimental Hepatocarcinoma. Cells 2024; 13:1013. [PMID: 38920644 PMCID: PMC11201610 DOI: 10.3390/cells13121013] [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: 03/27/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Hepatocellular carcinoma (HCC) development is associated with altered modifications in DNA methylation, changing transcriptional regulation. Emerging evidence indicates that DNA methyltransferase 1 (DNMT1) plays a key role in the carcinogenesis process. This study aimed to investigate how pirfenidone (PFD) modifies this pathway and the effect generated by the association between c-Myc expression and DNMT1 activation. Rats F344 were used for HCC development using 50 mg/kg of diethylnitrosamine (DEN) and 25 mg/kg of 2-Acetylaminofluorene (2-AAF). The HCC/PFD group received simultaneous doses of 300 mg/kg of PFD. All treatments lasted 12 weeks. On the other hand, HepG2 cells were used to evaluate the effects of PFD in restoring DNA methylation in the presence of the inhibitor 5-Aza. Histopathological, biochemical, immunohistochemical, and western blot analysis were carried out and our findings showed that PFD treatment reduced the amount and size of tumors along with decreased Glipican-3, β-catenin, and c-Myc expression in nuclear fractions. Also, this treatment improved lipid metabolism by modulating PPARγ and SREBP1 signaling. Interestingly, PFD augmented DNMT1 and DNMT3a protein expression, which restores global methylation, both in our in vivo and in vitro models. In conclusion, our results suggest that PFD could slow down HCC development by controlling DNA methylation.
Collapse
MESH Headings
- Animals
- DNA (Cytosine-5-)-Methyltransferase 1/metabolism
- DNA (Cytosine-5-)-Methyltransferase 1/genetics
- DNA Methylation/drug effects
- DNA Methylation/genetics
- Pyridones/pharmacology
- Rats
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Humans
- Hep G2 Cells
- Proliferating Cell Nuclear Antigen/metabolism
- Male
- Rats, Inbred F344
- Liver Neoplasms/drug therapy
- Liver Neoplasms/pathology
- Liver Neoplasms/genetics
- Gene Expression Regulation, Neoplastic/drug effects
- Diethylnitrosamine
- Liver Neoplasms, Experimental/drug therapy
- Liver Neoplasms, Experimental/pathology
- Liver Neoplasms, Experimental/metabolism
- Liver Neoplasms, Experimental/genetics
Collapse
Affiliation(s)
- Hipolito Otoniel Miranda-Roblero
- Programa de Doctorado en Ciencias en Biología Molecular en Medicina, CUCS, University of Guadalajara, Guadalajara 44340, Mexico; (H.O.M.-R.); (L.F.S.-S.)
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Liliana Faridi Saavedra-Salazar
- Programa de Doctorado en Ciencias en Biología Molecular en Medicina, CUCS, University of Guadalajara, Guadalajara 44340, Mexico; (H.O.M.-R.); (L.F.S.-S.)
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Marina Galicia-Moreno
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Scarlet Arceo-Orozco
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Fernando Caloca-Camarena
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Ana Sandoval-Rodriguez
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Jesús García-Bañuelos
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Claudia Frias-Gonzalez
- Programa de Doctorado en Ciencias en Biología Molecular en Medicina, CUCS, University of Guadalajara, Guadalajara 44340, Mexico; (H.O.M.-R.); (L.F.S.-S.)
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Mónica Almeida-López
- University Center of Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico
| | - Erika Martínez-López
- Institute of Translational Nutrigenetics and Nutrigenomics, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico
| | - Juan Armendariz-Borunda
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Zapopan 45138, Mexico
| | - Hugo Christian Monroy-Ramirez
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| |
Collapse
|
10
|
Yu C, Wu Q, Xin J, Yu Q, Ma Z, Xue M, Xu Q, Zheng C. Designing a smallpox B-cell and T-cell multi-epitope subunit vaccine using a comprehensive immunoinformatics approach. Microbiol Spectr 2024; 12:e0046524. [PMID: 38700327 DOI: 10.1128/spectrum.00465-24] [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: 02/19/2024] [Accepted: 04/01/2024] [Indexed: 05/05/2024] Open
Abstract
Smallpox is a highly contagious human disease caused by the variola virus. Although the disease was eliminated in 1979 due to its highly contagious nature and historical pathogenicity, with a mortality rate of up to 30%, this virus is an important candidate for biological weapons. Currently, vaccines are the critical measures to prevent this virus infection and spread. In this study, we designed a peptide vaccine using immunoinformatics tools, which have the potential to activate human immunity against variola virus infection efficiently. The design of peptides derives from vaccine-candidate proteins showing protective potential in vaccinia WR strains. Potential non-toxic and nonallergenic T-cell and B-cell binding and cytokine-inducing epitopes were then screened through a priority prediction using special linkers to connect B-cell epitopes and T-cell epitopes, and an appropriate adjuvant was added to the vaccine construction to enhance the immunogenicity of the peptide vaccine. The 3D structure display, docking, and free energy calculation analysis indicate that the binding affinity between the vaccine peptide and Toll-like receptor 3 is high, and the vaccine receptor complex is highly stable. Notably, the vaccine we designed is obtained from the protective protein of the vaccinia and combined with preventive measures to avoid side effects. This vaccine is highly likely to produce an effective and safe immune response against the variola virus infection in the body. IMPORTANCE In this work, we designed a vaccine with a cluster of multiple T-cell/B-cell epitopes, which should be effective in inducing systematic immune responses against variola virus infection. Besides, this work also provides a reference in vaccine design for preventing monkeypox virus infection, which is currently prevalent.
Collapse
Affiliation(s)
- Changqing Yu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Engineering Center of Agricultural Biosafety Assessment and Biotechnology, School of Advanced Agricultural Sciences, Yibin Vocational and Technical College, Yibin, China
| | - Qi Wu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jiuqing Xin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Qiujuan Yu
- Department of Dermatology, The First People's Hospital of Mudanjiang, Mudanjiang, China
| | - Zhixin Ma
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qingyuan Xu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infection Diseases, University of Calgary, Calgary, Canada
| |
Collapse
|
11
|
Saini S, Pareekh S, Kumar Y. Investigating the structural impact of Omicron RBD mutation on antibody escape and receptor management. J Biomol Struct Dyn 2024; 42:4668-4678. [PMID: 37334729 DOI: 10.1080/07391102.2023.2222174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/01/2023] [Indexed: 06/20/2023]
Abstract
The SARS-CoV-2 Variant B.1.1.5291 evolved rapidly in late November 2021 from the existing mutants sparking fear worldwide owing to its infamous immune escape from a varied class of neutralising antibodies. To assess the structural behaviour of Omicron-Receptor Binding Domain (RBD) upon interacting with cross-reactive CR3022 antibody, we investigated the computational approach of structural engagement in B.1.1529 RBD and wild-type RBD with CR3022 antibody. The current study investigates the interacting interface between the RBDs and CR3022 to decipher the key residues accompanying the potential mutational landscape of SARS-CoV-2 variants. We conducted in-silico docking followed by molecular dynamics simulation analysis to examine the dynamic behaviour of protein-protein interactions. Furthermore, the study unleashed possible interactions post energy decomposition analysis via MM-GBSA. Conclusively, the mutational landscape of RBD eases in designing and discovering the effective neutralisation accompanied by development of a universal vaccine.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Samvedna Saini
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
| | - Savita Pareekh
- High Performance Computing (HPC) & AI Innovation Lab, Dell EMC, Bengaluru, India
| | - Yatender Kumar
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
| |
Collapse
|
12
|
Gayen A, Mukherjee A, Kumar K, Majumder S, Chakrabarti S, Mukherjee C. The mRNA-capping enzyme localizes to stress granules in the cytoplasm and maintains cap homeostasis of target mRNAs. J Cell Sci 2024; 137:jcs261578. [PMID: 38841902 DOI: 10.1242/jcs.261578] [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: 08/23/2023] [Accepted: 04/08/2024] [Indexed: 06/07/2024] Open
Abstract
The model of RNA stability has undergone a transformative shift with the revelation of a cytoplasmic capping activity that means a subset of transcripts are recapped autonomously of their nuclear counterparts. The present study demonstrates nucleo-cytoplasmic shuttling of the mRNA-capping enzyme (CE, also known as RNA guanylyltransferase and 5'-phosphatase; RNGTT), traditionally acknowledged for its nuclear localization and functions, elucidating its contribution to cytoplasmic capping activities. A unique nuclear export sequence in CE mediates XPO1-dependent nuclear export of CE. Notably, during sodium arsenite-induced oxidative stress, cytoplasmic CE (cCE) congregates within stress granules (SGs). Through an integrated approach involving molecular docking and subsequent co-immunoprecipitation, we identify eIF3b, a constituent of SGs, as an interactive associate of CE, implying that it has a potential role in guiding cCE to SGs. We measured the cap status of specific mRNA transcripts from U2OS cells that were non-stressed, stressed and recovered from stress, which indicated that cCE-target transcripts lost their caps during stress but remarkably regained cap stability during the recovery phase. This comprehensive study thus uncovers a novel facet of cytoplasmic CE, which facilitates cellular recovery from stress by maintaining cap homeostasis of target mRNAs.
Collapse
Affiliation(s)
- Anakshi Gayen
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
- CellBio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
| | - Avik Mukherjee
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
| | - Krishna Kumar
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal 700091, India
| | - Shubhra Majumder
- CellBio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, Council for Scientific and Industrial Research (CSIR) - Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal 700091, India
| | - Chandrama Mukherjee
- RNABio Lab, Institute of Health Sciences, Presidency University, Kolkata, West Bengal 700156, India
| |
Collapse
|
13
|
Saleki K, Aram C, Alijanizadeh P, Khanmirzaei MH, Vaziri Z, Ramzankhah M, Azadmehr A. Matrix metalloproteinase/Fas ligand (MMP/FasL) interaction dynamics in COVID-19: An in silico study and neuroimmune perspective. Heliyon 2024; 10:e30898. [PMID: 38803919 PMCID: PMC11128882 DOI: 10.1016/j.heliyon.2024.e30898] [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: 08/04/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Background The initiator of cytokine storm in Coronavirus disease (COVID-19) is still unknown. We recently suggested a complex interaction of matrix metalloproteinases (MMPs), Fas ligand (FasL), and viral entry factors could be responsible for the cytokine outrage In COVID-19. We explored the molecular dynamics of FasL/MMP7-9 in COVID-19 conditions in silico and provide neuroimmune insights for future. Methods We enrolled and analyzed a clinical cohort of COVID-19 patients, and recorded their blood Na + levels and temperature at admission. A blood-like molecular dynamics simulation (MDS) box was then built. Four conditions were studied; MMP7/FasL (healthy), MMP7/FasL (COVID-19), MMP9-FasL (healthy), and MMP9/FasL (COVID-19). MDS was performed by GROningen MAchine for Chemical Simulation (GROMACS). We analyzed bonds, short-range energies, and free binding energies to draw conclusions on the interaction of MMP7/MMP9 and FasL to gain insights into COVID-19 immunopathology. Genevestigator was used study RNA-seq/microarray expression data of MMPs in the cells of immune and nervous systems. Finally, epitopes of MMP/FasL complexes were identified as drug targets by machine learning (ML) tools. Results MMP7-FasL (Healthy), MMP7-FasL (COVID-19), MMP9-FasL (Healthy), and MMP9-FasL (COVID-19) systems showed 0, 1, 4, and 2 salt bridges, indicating MMP9 had more salt bridges. Moreover, in both COVID-19 and normal conditions, the number of interacting residues and surface area was higher for MMP9 compared to MMP7 group. The COVID-19 MMP9-FasL group had more H-bonds compared to MMP7-FasL group (12 vs. 7). 15 epitopes for FasL-MMP9 and 10 epitopes for FasL-MMP7 were detected. Extended MD simulation for 100 ns confirmed stronger binding of MMP9 based on Molecular Mechanics Generalized Borne Surface analysis (MM-GBSA) and Coul and Leonard-Jones (LJ) short-range energies. Conclusions MMP9 interacts stronger than MMP7 with FasL, however, both molecules maintained strong interaction through the MDS. We suggested epitopes for MMP-FasL complexes as valuable therapeutic targets in COVID-19. These data could be utilized in future immune drug and protein design and repurposing efforts.
Collapse
Affiliation(s)
- Kiarash Saleki
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- Department of e-Learning, Virtual School of Medical Education and Management, Shahid Beheshti University of Medical Sciences(SBMU), Tehran, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
- National Elite Foundation, Mazandaran Province Branch, Mazandaran, Iran
| | - Cena Aram
- Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Parsa Alijanizadeh
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Hossein Khanmirzaei
- School of Medicine, Tehran University of Medical Sciences, Babol, Iran
- Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Zahra Vaziri
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Ramzankhah
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
- USERN Office, Babol University of Medical Sciences, Babol, Iran
| | - Abbas Azadmehr
- National Elite Foundation, Mazandaran Province Branch, Mazandaran, Iran
- Department of Immunology, Babol University of Medical Sciences, Babol, Iran
| |
Collapse
|
14
|
Rawat S, Singh G, Prasad A. Investigating the Taenia solium Fatty Acid Binding Protein Superfamily for Their Immunological Outlook and Prospect for Therapeutic Targets. ACS OMEGA 2024; 9:22557-22572. [PMID: 38826528 PMCID: PMC11137695 DOI: 10.1021/acsomega.3c09253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 06/04/2024]
Abstract
Taenia solium, like other helminthic parasites, lacks key components of cellular machinery required for endogenous lipid biosynthesis. This deficiency compels the parasite to obtain all of its lipid requirements from its host. The passage of lipids across the cell membrane is tightly regulated. To facilitate effective lipid transport, the cestode parasite utilizes certain lipid binding proteins called FABPs. These FABPs bind with the lipid ligands and allow the transport of lipids across the membranes and into the cytosol. Here, by integrating a computational with homology protein prediction tools, we had identified five FABPs in the T. solium proteome. We confirmed their presence by RNA expression analysis of respective genes from the parasite's cysticerci transcript. During the molecular modeling and MD simulation studies, two of them, TsM_000544100 and TsM_001185100, were most stable. Furthermore, they had a robust interaction with the IgG1 molecule, as evidenced by MD simulation. In addition, by employing in silico screening, we had identified potential ligand interacting residues that are present on the probable druggable site. In combination with in vitro cysticidal assays, enalaprilat dihydrate showed efficacy against cysticerci, which suggests that FABPs play a significant role in the cysticercus life cycle. Together, we provided a detailed distribution of all FABPs expressed by T. solium cysticerci and the critical role of TsM_001185100 in cysticercus viability.
Collapse
Affiliation(s)
- Suraj
S. Rawat
- School
of Biosciences and Bioengineering, Indian
Institute of Technology Mandi, Mandi, Himachal Pradesh 175005, India
| | - Gagandeep Singh
- Dayanad
Medical College and Hospital, Ludhiana, Punjab 141001,India
| | - Amit Prasad
- School
of Biosciences and Bioengineering, Indian
Institute of Technology Mandi, Mandi, Himachal Pradesh 175005, India
- Indian
Knowledge System and Mental Health Centre, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175005, India
- Centre
for Human-Computer Interaction, Indian Institute
of Technology Mandi, Mandi, Himachal Pradesh 175005, India
| |
Collapse
|
15
|
Xu Z, Sadleir L, Goel H, Jiao X, Niu Y, Zhou Z, de Valles-Ibáñez G, Poke G, Hildebrand M, Lieffering N, Qin J, Yang Z. Genotype and phenotype correlation of PHACTR1-related neurological disorders. J Med Genet 2024; 61:536-542. [PMID: 38272663 DOI: 10.1136/jmg-2023-109638] [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: 09/14/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND PHACTR1 (phosphatase and actin regulators) plays a key role in cortical migration and synaptic activity by binding and regulating G-actin and PPP1CA. This study aimed to expand the genotype and phenotype of patients with de novo variants in PHACTR1 and analyse the impact of variants on protein-protein interaction. METHODS We identified seven patients with PHACTR1 variants by trio-based whole-exome sequencing. Additional two subjects were ascertained from two centres through GeneMatcher. The genotype-phenotype correlation was determined, and AlphaFold-Multimer was used to predict protein-protein interactions and interfaces. RESULTS Eight individuals carried missense variants and one had CNV in the PHACTR1. Infantile epileptic spasms syndrome (IESS) was the unifying phenotype in eight patients with missense variants of PHACTR1. They could present with other types of seizures and often exhibit drug-resistant epilepsy with a poor prognosis. One patient with CNV displayed a developmental encephalopathy phenotype. Using AlphaFold-Multimer, our findings indicate that PHACTR1 and G-actin-binding sequences overlap with PPP1CA at the RPEL3 domain, which suggests possible competition between PPP1CA and G-actin for binding to PHACTR1 through a similar polymerisation interface. In addition, patients carrying missense variants located at the PHACTR1-PPP1CA or PHACTR1-G-actin interfaces consistently exhibit the IESS phenotype. These missense variants are mostly concentrated in the overlapping sequence (RPEL3 domain). CONCLUSIONS Patients with variants in PHACTR1 can have a phenotype of developmental encephalopathy in addition to IESS. Moreover, our study confirmed that the variants affect the binding of PHACTR1 to G-actin or PPP1CA, resulting in neurological disorders in patients.
Collapse
Affiliation(s)
- Zhao Xu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Lynette Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Himanshu Goel
- Hunter Genetics, Waratah, New South Wales, Australia
| | - Xianru Jiao
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Yue Niu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zongpu Zhou
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Guillem de Valles-Ibáñez
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Gemma Poke
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Michael Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Heidelberg, Victoria, Australia
- Neuroscience Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, South Brisbane, Queensland, Australia
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington, New Zealand
| | - Jiong Qin
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| |
Collapse
|
16
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. J Phys Chem B 2024; 128:4696-4715. [PMID: 38696745 DOI: 10.1021/acs.jpcb.4c01341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
In this study, we combined AlphaFold-based atomistic structural modeling, microsecond molecular simulations, mutational profiling, and network analysis to characterize binding mechanisms of the SARS-CoV-2 spike protein with the host receptor ACE2 for a series of Omicron XBB variants including XBB.1.5, XBB.1.5+L455F, XBB.1.5+F456L, and XBB.1.5+L455F+F456L. AlphaFold-based structural and dynamic modeling of SARS-CoV-2 Spike XBB lineages can accurately predict the experimental structures and characterize conformational ensembles of the spike protein complexes with the ACE2. Microsecond molecular dynamics simulations identified important differences in the conformational landscapes and equilibrium ensembles of the XBB variants, suggesting that combining AlphaFold predictions of multiple conformations with molecular dynamics simulations can provide a complementary approach for the characterization of functional protein states and binding mechanisms. Using the ensemble-based mutational profiling of protein residues and physics-based rigorous calculations of binding affinities, we identified binding energy hotspots and characterized the molecular basis underlying epistatic couplings between convergent mutational hotspots. Consistent with the experiments, the results revealed the mediating role of the Q493 hotspot in the synchronization of epistatic couplings between L455F and F456L mutations, providing a quantitative insight into the energetic determinants underlying binding differences between XBB lineages. We also proposed a network-based perturbation approach for mutational profiling of allosteric communications and uncovered the important relationships between allosteric centers mediating long-range communication and binding hotspots of epistatic couplings. The results of this study support a mechanism in which the binding mechanisms of the XBB variants may be determined by epistatic effects between convergent evolutionary hotspots that control ACE2 binding.
Collapse
Affiliation(s)
- Nishank Raisinghani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| |
Collapse
|
17
|
Varenyk Y, Theodorakis PE, Pham DQH, Li MS, Krupa P. Exploring Structural Insights of Aβ42 and α-Synuclein Monomers and Heterodimer: A Comparative Study Using Implicit and Explicit Solvent Simulations. J Phys Chem B 2024; 128:4655-4669. [PMID: 38700150 PMCID: PMC11103699 DOI: 10.1021/acs.jpcb.4c00503] [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: 01/24/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Protein misfolding, aggregation, and fibril formation play a central role in the development of severe neurological disorders, including Alzheimer's and Parkinson's diseases. The structural stability of mature fibrils in these diseases is of great importance, as organisms struggle to effectively eliminate amyloid plaques. To address this issue, it is crucial to investigate the early stages of fibril formation when monomers aggregate into small, toxic, and soluble oligomers. However, these structures are inherently disordered, making them challenging to study through experimental approaches. Recently, it has been shown experimentally that amyloid-β 42 (Aβ42) and α-synuclein (α-Syn) can coassemble. This has motivated us to investigate the interaction between their monomers as a first step toward exploring the possibility of forming heterodimeric complexes. In particular, our study involves the utilization of various Amber and CHARMM force-fields, employing both implicit and explicit solvent models in replica exchange and conventional simulation modes. This comprehensive approach allowed us to assess the strengths and weaknesses of these solvent models and force fields in comparison to experimental and theoretical findings, ensuring the highest level of robustness. Our investigations revealed that Aβ42 and α-Syn monomers can indeed form stable heterodimers, and the resulting heterodimeric model exhibits stronger interactions compared to the Aβ42 dimer. The binding of α-Syn to Aβ42 reduces the propensity of Aβ42 to adopt fibril-prone conformations and induces significant changes in its conformational properties. Notably, in AMBER-FB15 and CHARMM36m force fields with the use of explicit solvent, the presence of Aβ42 significantly increases the β-content of α-Syn, consistent with the experiments showing that Aβ42 triggers α-Syn aggregation. Our analysis clearly shows that although the use of implicit solvent resulted in too large compactness of monomeric α-Syn, structural properties of monomeric Aβ42 and the heterodimer were preserved in explicit-solvent simulations. We anticipate that our study sheds light on the interaction between α-Syn and Aβ42 proteins, thus providing the atom-level model required to assess the initial stage of aggregation mechanisms related to Alzheimer's and Parkinson's diseases.
Collapse
Affiliation(s)
- Yuliia Varenyk
- Institute
of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Department
of Theoretical Chemistry, University of
Vienna, Vienna 1090, Austria
| | | | - Dinh Q. H. Pham
- Institute
of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute
of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Paweł Krupa
- Institute
of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| |
Collapse
|
18
|
Rahangdale R, Ghormode P, Tender T, Balireddy S, Birangal S, Kishore R, Mohammad FS, Pasupuleti M, Chandrashekar H R. Anti-HSV activity of nectin-1-derived peptides targeting HSV gD: an in-silico and in-vitro approach. J Biomol Struct Dyn 2024:1-14. [PMID: 38720617 DOI: 10.1080/07391102.2024.2349525] [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: 11/29/2023] [Accepted: 03/24/2024] [Indexed: 05/22/2024]
Abstract
Herpes simplex virus (HSV) infections affect a wide range of the global population. The emergence of resistance to the existing anti-HSV therapy highlights the necessity for an innovative strategy. The interaction of HSV gD with its main host receptor nectin-1 is a potential target for new antiviral drugs. The aim of this study was to develop a peptide derived from nectin-1 targeting HSV gD using the in-silico method and evaluate them for anti-HSV activity. Residues 59-133 of the Nectin-1 V-domain constitute the interaction interface with HSV gD. Bioinformatic tools viz., PEP-FOLD3, ClusPro 2.0, HawkDock and Desmond were used to model the peptide and confirm its binding specificity with HSV gD protein. The peptides with potential interactions were custom synthesized and anti-HSV activity was evaluated in vitro against HSV-1 and HSV-2 by CPE inhibition assay. Five peptide sequences were identified as exhibiting good interaction with HSV-gD proteins. Among them, peptide N1 (residues 76-90) offered maximum protection against HSV-1 (66.57%) and HSV-2 (71.12%) infections. Modification of the identified peptide through peptidomimetic approaches may further enhance the activity and stability of the identified peptide.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rakesh Rahangdale
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Parnavi Ghormode
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Tenzin Tender
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sridevi Balireddy
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sumit Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Raj Kishore
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
- Jawaharlal Nehru University, New Delhi, India
| | - Fayaz Shaik Mohammad
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Mukesh Pasupuleti
- Microbiology Division, Council of Scientific and Industrial Research, Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raghu Chandrashekar H
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| |
Collapse
|
19
|
Araujo-Abad S, Rizzuti B, Vidal M, Abian O, Fárez-Vidal ME, Velazquez-Campoy A, de Juan Romero C, Neira JL. Unveiling the Binding between the Armadillo-Repeat Domain of Plakophilin 1 and the Intrinsically Disordered Transcriptional Repressor RYBP. Biomolecules 2024; 14:561. [PMID: 38785968 PMCID: PMC11117474 DOI: 10.3390/biom14050561] [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: 04/11/2024] [Revised: 04/29/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Plakophilin 1 (PKP1), a member of the p120ctn subfamily of the armadillo (ARM)-repeat-containing proteins, is an important structural component of cell-cell adhesion scaffolds although it can also be ubiquitously found in the cytoplasm and the nucleus. RYBP (RING 1A and YY1 binding protein) is a multifunctional intrinsically disordered protein (IDP) best described as a transcriptional regulator. Both proteins are involved in the development and metastasis of several types of tumors. We studied the binding of the armadillo domain of PKP1 (ARM-PKP1) with RYBP by using in cellulo methods, namely immunofluorescence (IF) and proximity ligation assay (PLA), and in vitro biophysical techniques, namely fluorescence, far-ultraviolet (far-UV) circular dichroism (CD), and isothermal titration calorimetry (ITC). We also characterized the binding of the two proteins by using in silico experiments. Our results showed that there was binding in tumor and non-tumoral cell lines. Binding in vitro between the two proteins was also monitored and found to occur with a dissociation constant in the low micromolar range (~10 μM). Finally, in silico experiments provided additional information on the possible structure of the binding complex, especially on the binding ARM-PKP1 hot-spot. Our findings suggest that RYBP might be a rescuer of the high expression of PKP1 in tumors, where it could decrease the epithelial-mesenchymal transition in some cancer cells.
Collapse
Affiliation(s)
- Salome Araujo-Abad
- Cancer Research Group, Faculty of Engineering and Applied Sciences, Universidad de Las Américas, 170124 Quito, Ecuador;
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy;
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
| | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Calle Ramiro de Maeztu, 9, 28040 Madrid, Spain;
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - María Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain;
- Instituto de Investigación Biomédica IBS, Granada, Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Camino de Juan Romero
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l’Almazara 11, 03203 Elche, Spain
| | - José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
| |
Collapse
|
20
|
Glenet M, Lebreil AL, N'Guyen Y, Meyer I, Baud S, Andreoletti L. Structural impact of a new spike Y170W mutation detected in early emerging SARS-CoV-2 Omicron variants in France. Virus Res 2024; 343:199354. [PMID: 38492859 PMCID: PMC10957500 DOI: 10.1016/j.virusres.2024.199354] [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: 01/30/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
To assess the genetic characteristics of the early emerging SARS-CoV-2 Omicron variant strains, we retrospectively analyzed a collection of 150 nasopharyngeal samples taken from a series of outpatient cases tested positive by a referenced qRT-PCR assay during the reported period of Omicron variant emergence in December 2021, in northeastern region of France. Next Generation Sequencing (NGS) analysis of SARS-CoV-2 spike sequences revealed that only 3 (2 %) of these detected strains were Omicron variants, while 147 (98 %) were identified as previously described delta variants. Our phylogenetic analyzes of SARS-CoV-2 RNA genomes showed that these French early emerging Omicron variants may have originated from South Africa or India. In addition, whole viral genome sequences NGS comparison analyzes allowed us to identify an original and uncharacterized Y170W spike mutation that was weakly and transiently detected during the period of SARS-CoV-2 Omicron variant emergence in human populations. Molecular modeling and docking experiments indicated that this original mutated residue Y170W was neither directly involved in binding to the SARS-CoV-2 receptor ACE2 nor in interacting with known neutralizing antibody sites. However, this new mutation may be responsible for preventing the transition from the closed to the open Spike conformation, thus promoting the early emergence of the Omicron variant. Overall, these results underscore the epidemiological utility of a routine whole-genome viral NGS strategy that enables genotypic characterization of emerging or mutant SARS-CoV-2 variants, which could have significant implications for public health policy.
Collapse
Affiliation(s)
- Marie Glenet
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France.
| | - Anne-Laure Lebreil
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France
| | - Yohan N'Guyen
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France; Infectious Diseases and Internal Medicine Department, CHU Reims, Hôpital Robert Debré, Reims, France
| | - Ittah Meyer
- Unilabs BioCT, Private Laboratory Group, Château-Thierry, France
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, CNRS, MEDyC UMR 7369, Reims, France
| | - Laurent Andreoletti
- University of Reims Champagne-Ardenne, Laboratory of Virology, CardioVir UMR-S 1320 51 rue Cognacq Jay, REIMS Cedex, Reims 51092, France; Virology Department, CHU Reims, Hôpital Robert Debré, Reims, France
| |
Collapse
|
21
|
Huang F, Dai Q, Zheng K, Ma Q, Liu Y, Jiang S, Jiang W, Yan X. Exploring the inhibitory potential of KPHs-AL-derived GLLF peptide on pancreatic lipase and cholesterol esterase activities. Food Chem 2024; 439:138108. [PMID: 38061297 DOI: 10.1016/j.foodchem.2023.138108] [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: 09/15/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 01/10/2024]
Abstract
The effective modulation of pancreatic lipase and cholesterol esterase activities proves critical in maintaining circulatory triglycerides and cholesterol levels within physiological boundaries. In this study, peptides derived from KPHs-AL, produced through the enzymatic hydrolysis of skipjack tuna dark muscle using alkaline protease, have a specific inhibitory effect on pancreatic lipase and cholesterol esterase. It is hypothesized that these peptides target and modulate the activities of enzymes by inducing conformational changes within their binding pockets, potentially impacting the catalytic functions of both pancreatic lipase and cholesterol esterase. Results revealed these peptides including AINDPFIDL, FLGM, GLLF and WGPL, were found to nestle into the binding site groove of pancreatic lipase and cholesterol esterase. Among these, GLLF stood out, demonstrating potent inhibition with IC50 values of 0.1891 mg/mL and 0.2534 mg/mL for pancreatic lipase and cholesterol esterase, respectively. The kinetics studies suggested that GLLF competed effectively with substrates for the enzyme active sites. Spectroscopic analyses, including ultraviolet-visible, fluorescence quenching, and circular dichroism, indicated that GLLF binding induced conformational changes within the enzymes, likely through hydrogen bond formation and hydrophobic interactions, thereby increasing structural flexibility. Molecular docking and molecular dynamics simulations supported these findings, showing GLLF's stable interaction with vital active site residues. These findings position GLLF as a potent inhibitor of key digestive enzymes, offering insights into its role in regulating lipid metabolism and highlighting its potential as functional ingredient.
Collapse
Affiliation(s)
- Fangfang Huang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China; Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Qingfei Dai
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Kewei Zheng
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Qingbao Ma
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Yu Liu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Shuoqi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi, Jiangsu, China
| | - Wei Jiang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China.
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| |
Collapse
|
22
|
Eirich P, Nesterov P, Shityakov S, Skorb EV, Sander B, Broscheit J, Dandekar T, Jones NG, Engstler M. The release of host-derived antibodies bound to the variant surface glycoprotein (VSG) of Trypanosoma brucei cannot be explained by pH-dependent conformational changes of the VSG dimer. OPEN RESEARCH EUROPE 2024; 4:87. [PMID: 38903703 PMCID: PMC11187536 DOI: 10.12688/openreseurope.16783.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/26/2024] [Indexed: 06/22/2024]
Abstract
Background Trypanosoma brucei is a protozoan parasite that evades the mammalian host's adaptive immune response by antigenic variation of the highly immunogenic variant surface glycoprotein (VSG). VSGs form a dense surface coat that is constantly recycled through the endosomal system. Bound antibodies are separated in the endosome from the VSG and destroyed in the lysosome. For VSGs it has been hypothesized that pH-dependent structural changes of the VSG could occur in the more acidic environment of the endosome and hence, facilitate the separation of the antibody from the VSG. Methods We used size exclusion chromatography, where molecules are separated according to their hydrodynamic radius to see if the VSG is present as a homodimer at both pH values. To gain information about the structural integrity of the protein we used circular dichroism spectroscopy by exposing the VSG in solution to a mixture of right- and left-circularly polarized light and analysing the absorbed UV spectra. Evaluation of protein stability and molecular dynamics simulations at different pH values was performed using different computational methods. Results We show, for an A2-type VSG, that the dimer size is only slightly larger at pH 5.2 than at pH 7.4. Moreover, the dimer was marginally more stable at lower pH due to the higher affinity (ΔG = 353.37 kcal/mol) between the monomers. Due to the larger size, the predicted epitopes were more exposed to the solvent at low pH. Moderate conformational changes (ΔRMSD = 0.35 nm) in VSG were detected between the dimers at pH 5.2 and pH 7.4 in molecular dynamics simulations, and no significant differences in the protein secondary structure were observed by circular dichroism spectroscopy. Conclusions Thus, the dissociation of anti-VSG-antibodies in endosomes cannot be explained by changes in pH.
Collapse
Affiliation(s)
- Patrick Eirich
- Department of Cell & Developmental Biology, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, Würzburg University Hospital, University of Würzburg, Würzburg, Bavaria, 97080, Germany
| | - Pavel Nesterov
- Infochemistry Scientific Center, Laboratory of Chemoinformatics, ITMO University, Saint Petersburg, Saint Petersburg, 191002, Russian Federation
| | - Sergey Shityakov
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, Würzburg University Hospital, University of Würzburg, Würzburg, Bavaria, 97080, Germany
- Infochemistry Scientific Center, Laboratory of Chemoinformatics, ITMO University, Saint Petersburg, Saint Petersburg, 191002, Russian Federation
- Department of Bioinformatics, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
| | - Ekaterina V. Skorb
- Infochemistry Scientific Center, Laboratory of Chemoinformatics, ITMO University, Saint Petersburg, Saint Petersburg, 191002, Russian Federation
| | - Bodo Sander
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Bavaria, 97080, Germany
| | - Jens Broscheit
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, Würzburg University Hospital, University of Würzburg, Würzburg, Bavaria, 97080, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
| | - Nicola G. Jones
- Department of Cell & Developmental Biology, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
| | - Markus Engstler
- Department of Cell & Developmental Biology, Biocentre, University of Würzburg, Würzburg, Bavaria, 97074, Germany
| |
Collapse
|
23
|
Papanikolaou NA, Kakavoulia M, Ladias C, Papavassiliou AG. The ras-related protein RAB22A interacts with hypoxia-inducible factor 1-alpha (HIF-1α) in MDA-MB-231 breast cancer cells in hypoxia. Mol Biol Rep 2024; 51:564. [PMID: 38647725 DOI: 10.1007/s11033-024-09516-3] [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: 02/24/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Recent studies suggest that hypoxia-inducible factor 1-alpha (HIF-1α) and the small GTPase protein Ras-related protein Rab-22 A (RAB22A) may be colocalized in the cytoplasm and that as a conequence they may enhance the formation of microvesicles in breast cancer cells under hypoxia. Therefore, we sought to determine whether these two proteins are present in intracellular complexes in breast carcinoma cells. METHODS AND RESULTS Evaluation using molecular docking indicated that HIF-1α and RAB22A interact with each other. Co-immunoprecipitation of endogenous or ectopically expressed HIF-1α and RAB22A proteins in MDA-MB-231 breast cancer cells or HEK-293T cells demonstrated that endogenous HIF-1α and RAB22A can form an intracellular complex; however, transiently expressed HIF-1α and RAB22A failed to interact. Investigating RAB22A and HIF-1α interactions in various cancer cell lines under hypoxia may shed light on their roles in cancer cell survival and progression through regulation of intracellular trafficking by HIF-1α under hypoxic conditions. CONCLUSIONS Our study is the first to reveal the potential involvement of HIF-1α in intracellular trafficking through physical interactions with the small GTPase protein RAB22A. We discuss the implications of our work on the role of exosomes and microvesicles in tumor invasiveness.
Collapse
Affiliation(s)
- Nikolaos A Papanikolaou
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece.
| | - Maria Kakavoulia
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece
| | - Christos Ladias
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Epirus, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
| |
Collapse
|
24
|
Panda SK, Karmakar S, Sen Gupta PS, Rana MK. Can Duvelisib and Eganelisib work for both cancer and COVID-19? Molecular-level insights from MD simulations and enhanced samplings. Phys Chem Chem Phys 2024; 26:10961-10973. [PMID: 38526354 DOI: 10.1039/d3cp05934k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
SARS-CoV-2 has caused severe illness and anxiety worldwide, evolving into more dreadful variants capable of evading the host's immunity. Cytokine storms, led by PI3Kγ, are common in cancer and SARS-CoV-2. Naturally, there is a yearning to see whether any drugs could alleviate cytokine storms for both. Upon investigation, we identified two anticancer drugs, Duvelisib and Eganelisib, that could also work against SARS-CoV-2. This report is the first to decipher their synergic therapeutic effectiveness against COVID-19 and cancer with molecular insights from atomistic simulations. In addition to PI3Kγ, these drugs exhibit specificity for the main protease among all SARS-CoV-2 targets, with significant negative binding free energies and small time-dependent conformational changes of the complexes. Complexation makes active sites and secondary structures highly mechanically stiff, with barely any deformation. Replica simulations estimated large pulling forces in enhanced sampling to dissociate the drugs from Mpro's active site. Furthermore, the radial distribution function (RDF) demonstrated that the therapeutic molecules were closest to the His41 and Cys145 catalytic dyad residues. Finally, analyses implied Duvelisib and Eganelisib as promising dual-purposed anti-COVID and anticancer drugs, potentially targeting Mpro and PI3Kγ to stop virus replication and cytokine storms concomitantly. We also distinguished hotspot residues imparting significant interactions.
Collapse
Affiliation(s)
- Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Shaswata Karmakar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| |
Collapse
|
25
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587850. [PMID: 38617283 PMCID: PMC11014522 DOI: 10.1101/2024.04.02.587850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
In this study, we combined AlphaFold-based approaches for atomistic modeling of multiple protein states and microsecond molecular simulations to accurately characterize conformational ensembles and binding mechanisms of convergent evolution for the SARS-CoV-2 Spike Omicron variants BA.1, BA.2, BA.2.75, BA.3, BA.4/BA.5 and BQ.1.1. We employed and validated several different adaptations of the AlphaFold methodology for modeling of conformational ensembles including the introduced randomized full sequence scanning for manipulation of sequence variations to systematically explore conformational dynamics of Omicron Spike protein complexes with the ACE2 receptor. Microsecond atomistic molecular dynamic simulations provide a detailed characterization of the conformational landscapes and thermodynamic stability of the Omicron variant complexes. By integrating the predictions of conformational ensembles from different AlphaFold adaptations and applying statistical confidence metrics we can expand characterization of the conformational ensembles and identify functional protein conformations that determine the equilibrium dynamics for the Omicron Spike complexes with the ACE2. Conformational ensembles of the Omicron RBD-ACE2 complexes obtained using AlphaFold-based approaches for modeling protein states and molecular dynamics simulations are employed for accurate comparative prediction of the binding energetics revealing an excellent agreement with the experimental data. In particular, the results demonstrated that AlphaFold-generated extended conformational ensembles can produce accurate binding energies for the Omicron RBD-ACE2 complexes. The results of this study suggested complementarities and potential synergies between AlphaFold predictions of protein conformational ensembles and molecular dynamics simulations showing that integrating information from both methods can potentially yield a more adequate characterization of the conformational landscapes for the Omicron RBD-ACE2 complexes. This study provides insights in the interplay between conformational dynamics and binding, showing that evolution of Omicron variants through acquisition of convergent mutational sites may leverage conformational adaptability and dynamic couplings between key binding energy hotspots to optimize ACE2 binding affinity and enable immune evasion.
Collapse
|
26
|
Darvishi F, Beiranvand E, Kalhor H, Shahbazi B, Mafakher L. Homology modeling and molecular docking studies to decrease glutamine affinity of Yarrowia lipolytica L-asparaginase. Int J Biol Macromol 2024; 263:130312. [PMID: 38403216 DOI: 10.1016/j.ijbiomac.2024.130312] [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: 10/13/2023] [Revised: 01/10/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
L-Asparaginase is a key component in the treatment of leukemias and lymphomas. However, the glutamine affinity of this therapeutic enzyme is an off-target activity that causes several side effects. The modeling and molecular docking study of Yarrowia lipolytica L-asparaginase (YL-ASNase) to reduce its l-glutamine affinity and increase its stability was the aim of this study. Protein-ligand interactions of wild-type and different mutants of YL-ASNase against L-asparagine compared to l-glutamine were assessed using AutoDock Vina tools because the crystal structure of YL-ASNase does not exist in the protein data banks. The results showed that three mutants, T171S, T171S-N60A, and T171A-T223A, caused a considerable increase in L-asparagine affinity and a decrease in l-glutamine affinity as compared to the wild-type and other mutants. Then, molecular dynamics simulation and MM/GBSA free energy were applied to assess the stability of protein structure and its interaction with ligands. The three mutated proteins, especially T171S-N60A, had higher stability and interactions with L-asparagine than l-glutamine in comparison with the wild-type. The YL-ASNase mutants could be introduced as appropriate therapeutic candidates that might cause lower side effects. However, the functional properties of these mutated enzymes need to be confirmed by genetic manipulation and in vitro and in vivo studies.
Collapse
Affiliation(s)
- Farshad Darvishi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology (CAMB), Alzahra University, Tehran, Iran.
| | - Elham Beiranvand
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Hourieh Kalhor
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Behzad Shahbazi
- School of Pharmacy, Semnan University of Medical Sciences, Semnan, Iran
| | - Ladan Mafakher
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| |
Collapse
|
27
|
Alsaiari AA, Hakami MA, Alotaibi BS, Alkhalil SS, Hazazi A, Alkhorayef N, Jalal K, Yasmin F. Rational design of multi-epitope-based vaccine by exploring all dengue virus serotypes proteome: an immunoinformatic approach. Immunol Res 2024; 72:242-259. [PMID: 37880483 DOI: 10.1007/s12026-023-09429-6] [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: 07/14/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Millions of people's lives are being devastated by dengue virus (DENV), a severe tropical and subtropical illness spread by mosquitoes and other vectors. Dengue fever may be self-limiting like a common cold or can rapidly progress to catastrophic dengue hemorrhagic fever or dengue shock syndrome. With four distinct dengue serotypes (DENV1-4), each with the potential to contain antibody-boosting complicated mechanisms, developing a dengue vaccine has been an ambitious challenge. Here, we used a computational pan-vaccinomics-based vaccine design strategy (reverse vaccinology) for all 4 DENV serotypes acquired from different regions of the world to develop a new and safe vaccine against DENV. Consequently, only five mapped epitopes from all the 4 serotypes were shown to be extremely effective for the construction of multi-epitope vaccine constructs. The suggested vaccine construct V5 from eight vaccine models was thus classified as an antigenic, non-allergenic, and stable vaccine model. Moreover, molecular docking and molecular dynamics simulation was performed for the V5 vaccine candidate against the HLAs and TRL2 and 4 immunological receptors. Later, the vaccine sequence was transcribed into the cDNA to generate an expression vector for the Escherichia coli K12 strain. Our research suggests that this vaccine design (V5) has promising potential as a dengue vaccine. However, further experimental analysis into the vaccine's efficacy might be required for the V5 proper validation to combat all DENV serotypes.
Collapse
Affiliation(s)
- Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, 15572, Saudi Arabia
| | - Bader S Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, 15572, Saudi Arabia
| | - Samia S Alkhalil
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, 15572, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Kingdom of Saudi Arabia
| | - Nada Alkhorayef
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, 15572, Saudi Arabia
| | - Khurshid Jalal
- H.E.J. Research Institute of Chemistry, University of Karachi, Karachi, 75270, Pakistan.
- Department of Mental Health and Public Health, Faculty of Life and Health Sciences, Shenzhen Institute of Advance Technology, Chinese Academy of Sciences, Shenzhen, 518055, Guangdong, China.
| | - Farzana Yasmin
- Department of Biomedical Engineering, NED University of Engineering and Technology, Karachi, 75270, Pakistan.
| |
Collapse
|
28
|
Carrión-Estrada DA, Aguilar-Rojas A, Huerta-Yepez S, Montecillo-Aguado M, Bello M, Rojo-Domínguez A, Arechaga-Ocampo E, Briseño-Díaz P, Meraz-Ríos MA, Thompson-Bonilla MDR, Hernández-Rivas R, Vargas M. Antineoplastic effect of compounds C14 and P8 on TNBC and radioresistant TNBC cells by stabilizing the K-Ras4B G13D/PDE6δ complex. Front Oncol 2024; 14:1341766. [PMID: 38571493 PMCID: PMC10989073 DOI: 10.3389/fonc.2024.1341766] [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: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 04/05/2024] Open
Abstract
Introduction Breast cancer (BC) is the leading cause of cancer-related deaths among women, with triple-negative breast cancer (TNBC) representing one of the most aggressive and treatment-resistant subtypes. In this study, we aimed to evaluate the antitumor potential of C14 and P8 molecules in both TNBC and radioresistant TNBC cells. These compounds were chosen for their ability to stabilize the complex formed by the overactivated form of K-Ras4BG13D and its membrane transporter (PDE6δ). Methods The antitumor potential of C14 and P8 was assessed using TNBC cell lines, MDA-MB-231, and the radioresistant derivative MDA-MB-231RR, both carrying the K-Ras4B> G13D mutation. We investigated the compounds' effects on K-Ras signaling pathways, cell viability, and tumor growth in vivo. Results Western blotting analysis determined the negative impact of C14 and P8 on the activation of mutant K-Ras signaling pathways in MDA-MB-231 and MDA-MB-231RR cells. Proliferation assays demonstrated their efficacy as cytotoxic agents against K-RasG13D mutant cancer cells and in inducing apoptosis. Clonogenic assays proven their ability to inhibit TNBC and radioresistant TNBC cell clonogenicity. In In vivo studies, C14 and P8 inhibited tumor growth and reduced proliferation, angiogenesis, and cell cycle progression markers. Discussion These findings suggest that C14 and P8 could serve as promising adjuvant treatments for TNBC, particularly for non-responders to standard therapies. By targeting overactivated K-Ras and its membrane transporter, these compounds offer potential therapeutic benefits against TNBC, including its radioresistant form. Further research and clinical trials are warranted to validate their efficacy and safety as novel TNBC treatments.
Collapse
Affiliation(s)
- Dayan A. Carrión-Estrada
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-I.P.N.), Mexico City, Mexico
| | - Arturo Aguilar-Rojas
- Medical Research Unit in Reproductive Medicine, Mexican Social Security Institute (IMSS), High Specialty Medical Unit in Gynecology and Obstetrics No. 4 Dr. Luis Castelazo Ayala, Mexico City, Mexico
| | - Sara Huerta-Yepez
- Research Unit in Oncological Diseases, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Mayra Montecillo-Aguado
- Research Unit in Oncological Diseases, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Martiniano Bello
- Laboratory for the Design and Development of New Drugs and Biotechnological Innovation, Higher School of Medicine, National Polytechnic Institute, Mexico City, Mexico
| | - Arturo Rojo-Domínguez
- Department of Natural Sciences, Metropolitan Autonomous University Cuajimalpa Unit, Mexico City, Mexico
| | - Elena Arechaga-Ocampo
- Department of Natural Sciences, Metropolitan Autonomous University Cuajimalpa Unit, Mexico City, Mexico
| | - Paola Briseño-Díaz
- Department of Biochemistry of the Faculty of Medicine of the National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Marco Antonio Meraz-Ríos
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-I.P.N.), Mexico City, Mexico
| | - María del Rocío Thompson-Bonilla
- Biomedical and Transnational Research, Genomic Medicine Laboratory, Hospital 1° de Octubre, Institute of Security and Social Services of State Workers (ISSSTE), Mexico City, Mexico
| | - Rosaura Hernández-Rivas
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-I.P.N.), Mexico City, Mexico
| | - Miguel Vargas
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-I.P.N.), Mexico City, Mexico
| |
Collapse
|
29
|
Wang Y, Buck A, Piel B, Zerefa L, Murugan N, Coherd CD, Miklosi AG, Johal H, Bastos RN, Huang K, Ficial M, Laimon YN, Signoretti S, Zhong Z, Hoang SM, Kastrunes GM, Grimaud M, Fayed A, Yuan HC, Nguyen QD, Thai T, Ivanova EV, Paweletz CP, Wu MR, Choueiri TK, Wee JO, Freeman GJ, Barbie DA, Marasco WA. Affinity fine-tuning anti-CAIX CAR-T cells mitigate on-target off-tumor side effects. Mol Cancer 2024; 23:56. [PMID: 38491381 PMCID: PMC10943873 DOI: 10.1186/s12943-024-01952-w] [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: 10/23/2023] [Accepted: 01/31/2024] [Indexed: 03/18/2024] Open
Abstract
One of the major hurdles that has hindered the success of chimeric antigen receptor (CAR) T cell therapies against solid tumors is on-target off-tumor (OTOT) toxicity due to sharing of the same epitopes on normal tissues. To elevate the safety profile of CAR-T cells, an affinity/avidity fine-tuned CAR was designed enabling CAR-T cell activation only in the presence of a highly expressed tumor associated antigen (TAA) but not when recognizing the same antigen at a physiological level on healthy cells. Using direct stochastic optical reconstruction microscopy (dSTORM) which provides single-molecule resolution, and flow cytometry, we identified high carbonic anhydrase IX (CAIX) density on clear cell renal cell carcinoma (ccRCC) patient samples and low-density expression on healthy bile duct tissues. A Tet-On doxycycline-inducible CAIX expressing cell line was established to mimic various CAIX densities, providing coverage from CAIX-high skrc-59 tumor cells to CAIX-low MMNK-1 cholangiocytes. Assessing the killing of CAR-T cells, we demonstrated that low-affinity/high-avidity fine-tuned G9 CAR-T has a wider therapeutic window compared to high-affinity/high-avidity G250 that was used in the first anti-CAIX CAR-T clinical trial but displayed serious OTOT effects. To assess the therapeutic effect of G9 on patient samples, we generated ccRCC patient derived organotypic tumor spheroid (PDOTS) ex vivo cultures and demonstrated that G9 CAR-T cells exhibited superior efficacy, migration and cytokine release in these miniature tumors. Moreover, in an RCC orthotopic mouse model, G9 CAR-T cells showed enhanced tumor control compared to G250. In summary, G9 has successfully mitigated OTOT side effects and in doing so has made CAIX a druggable immunotherapeutic target.
Collapse
Affiliation(s)
- Yufei Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Alicia Buck
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Brandon Piel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Luann Zerefa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nithyassree Murugan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Christian D Coherd
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | | | | | - Kun Huang
- Molecular Imaging Core, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Miriam Ficial
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Yasmin Nabil Laimon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sabina Signoretti
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | | | - Gabriella M Kastrunes
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marion Grimaud
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Atef Fayed
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Hsien-Chi Yuan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tran Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elena V Ivanova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Belfer Center of Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Cloud P Paweletz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Belfer Center of Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ming-Ru Wu
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Toni K Choueiri
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jon O Wee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gordon J Freeman
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David A Barbie
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Belfer Center of Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Wayne A Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
30
|
Wang W, Chen X, Chen J, Xu M, Liu Y, Yang S, Zhao W, Tan S. Engineering lentivirus envelope VSV-G for liver targeted delivery of IDOL-shRNA to ameliorate hypercholesterolemia and atherosclerosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102115. [PMID: 38314097 PMCID: PMC10835450 DOI: 10.1016/j.omtn.2024.102115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024]
Abstract
Lentiviral vectors (LVs) have been widely used as a tool for gene therapies. However, tissue-selective transduction after systemic delivery remains a challenge. Inducible degrader of low-density lipoprotein receptor is an attractive target for treating hypercholesterolemia. Here, a liver-targeted LV, CS8-LV-shIDOL, is developed by incorporating a hepatocyte-targeted peptide derived from circumsporozoite protein (CSP) into the lentivirus envelope for liver-targeted delivery of IDOL-shRNA (short hairpin RNA) to alleviate hypercholesterolemia. Tail-vein injection of CS8-LV-shIDOL results in extremely high accumulation in liver and nearly undetectable levels in other organs in mice. In addition, it shows superior therapeutic efficacy in lowering serum low-density lipoprotein cholesterol (LDL-C) and reducing atherosclerotic lesions over unmodified LV-shIDOL in hyperlipidemic mice. Mechanically, the envelope-engineered CS8-LV-shIDOL can enter liver cells via low-density lipoprotein receptor-related protein (LRP). Thus, this study provides a novel approach for liver-targeted delivery of IDOL-shRNA to treat hypercholesterolemia by using an envelope-engineered LV, and this delivery system has great potential for liver-targeted transgene therapy.
Collapse
Affiliation(s)
- Wei Wang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Xuemei Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Jiali Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Menglong Xu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Ying Liu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Shijie Yang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Wenfeng Zhao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| | - Shuhua Tan
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
31
|
Tan C, Zhou J, Wu A, Li C. In silico development of a novel anti-mutation, multi-epitope mRNA vaccine against MPXV variants of emerging lineage and sub-lineages by using immunoinformatics approaches. J Biomol Struct Dyn 2024:1-18. [PMID: 38450722 DOI: 10.1080/07391102.2024.2325109] [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: 10/26/2023] [Accepted: 02/24/2024] [Indexed: 03/08/2024]
Abstract
Over the past year, an unexpected surge in human monkeypox (hMPX) cases has been observed. This outbreak differs from previous ones, displaying distinct epidemiological characteristics and transmission patterns, believed to be influenced by a newly emerging monkeypox virus (MPXV) lineage. Notably, this emerging MPXV lineage has exhibited several non-synonymous mutations, some of which are linked to immunomodulatory activities and antigenic characteristics that aid in host detection. However, specific treatments or vaccines for human monkeypox are currently lacking. Hence, we aim to develop a multi-epitope mRNA vaccine by using immunoinformatics approaches against the MPXV, particularly its emerging variants. Six proteins (A29L, A35R, B6R, M1R, H3L, and E8L) were chosen for epitope and mutation site identification. Seventeen top-performing epitopes and eight epitopes containing mutation sites were selected and combined with adjuvants, the PADRE sequence, and linkers for vaccine development. The molecular and physical properties of the designed vaccine (WLmpx) were favorable. Immunological characteristics of WLmpx were assessed through molecular docking, molecular dynamics (MD) simulations, and immune simulations. Finally, the vaccine sequence was utilized to formulate an mRNA-based vaccine. The informatics-based predicted results indicated that the designed vaccine exhibits significant potential in eliciting high-level humoral and cellular immune responses, but further validation through in vivo and vitro studies is warranted.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Caixia Tan
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, China
| | - Jingxiang Zhou
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, China
| |
Collapse
|
32
|
Radka CD, Rock CO. Crystal structures of the fatty acid biosynthesis initiation enzymes in Bacillus subtilis. J Struct Biol 2024; 216:108065. [PMID: 38310992 PMCID: PMC10939784 DOI: 10.1016/j.jsb.2024.108065] [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: 12/16/2023] [Revised: 01/10/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
Bacteria use the fatty acid composition of membrane lipids to maintain homeostasis of the bilayer. β-Ketoacyl-ACP synthase III (FabH) initiates fatty acid biosynthesis and is the primary determinant of the fatty acid composition. FabH condenses malonyl-acyl carrier protein with an acyl-Coenzyme A primer to form β -ketoacyl-acyl carrier protein which is used to make substrates for lipid synthesis. The acyl-Coenzyme A primer determines whether an acyl chain in the membrane has iso, anteiso, or no branching (straight chain) and biophysical properties of the membrane. The soil bacterium Bacillus subtilis encodes two copies of FabH (BsFabHA and BsFabHB), and here we solve their crystal structures. The substrate-free 1.85 Å and 2.40 Å structures of BsFabHA and BsFabHB show both enzymes have similar residues that line the active site but differ in the architecture surrounding the catalytic residues and oxyanion hole. Branching in the BsFabHB active site may better accommodate the structure of an iso-branched acyl-Coenzyme A molecule and thus confer superior utilization to BsFabHA for this primer type. The 2.02 Å structure of BsFabHA•Coenzyme A shows how the active site architecture changes after binding the first substrate. The other notable difference is an amino acid insertion in BsFabHB that extends a cap that covers the dimer interface. The cap topology is diverse across FabH structures and appears to be a distinguishing feature. FabH enzymes have variable sensitivity to natural product inhibitors and the availability of crystal structures help clarify how nature designs antimicrobials that differentially target FabH homologs.
Collapse
Affiliation(s)
- Christopher D Radka
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, 760 Press Avenue, Lexington, KY 40536, USA.
| | - Charles O Rock
- Department of Host Microbe Interactions, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| |
Collapse
|
33
|
Schoenaers S, Lee HK, Gonneau M, Faucher E, Levasseur T, Akary E, Claeijs N, Moussu S, Broyart C, Balcerowicz D, AbdElgawad H, Bassi A, Damineli DSC, Costa A, Feijó JA, Moreau C, Bonnin E, Cathala B, Santiago J, Höfte H, Vissenberg K. Rapid alkalinization factor 22 has a structural and signalling role in root hair cell wall assembly. NATURE PLANTS 2024; 10:494-511. [PMID: 38467800 DOI: 10.1038/s41477-024-01637-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024]
Abstract
Pressurized cells with strong walls make up the hydrostatic skeleton of plants. Assembly and expansion of such stressed walls depend on a family of secreted RAPID ALKALINIZATION FACTOR (RALF) peptides, which bind both a membrane receptor complex and wall-localized LEUCINE-RICH REPEAT EXTENSIN (LRXs) in a mutually exclusive way. Here we show that, in root hairs, the RALF22 peptide has a dual structural and signalling role in cell expansion. Together with LRX1, it directs the compaction of charged pectin polymers at the root hair tip into periodic circumferential rings. Free RALF22 induces the formation of a complex with LORELEI-LIKE-GPI-ANCHORED PROTEIN 1 and FERONIA, triggering adaptive cellular responses. These findings show how a peptide simultaneously functions as a structural component organizing cell wall architecture and as a feedback signalling molecule that regulates this process depending on its interaction partners. This mechanism may also underlie wall assembly and expansion in other plant cell types.
Collapse
Affiliation(s)
- Sébastjen Schoenaers
- Department of Biology, Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Institut Jean-Pierre Bourgin, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Hyun Kyung Lee
- Department of Plant Molecular Biology, The Plant Signaling Mechanisms Laboratory, University of Lausanne, Lausanne, Switzerland
| | - Martine Gonneau
- Institut Jean-Pierre Bourgin, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Elvina Faucher
- Institut Jean-Pierre Bourgin, AgroParisTech, Université Paris-Saclay, Versailles, France
| | | | - Elodie Akary
- Institut Jean-Pierre Bourgin, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Naomi Claeijs
- Department of Biology, Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
| | - Steven Moussu
- Department of Plant Molecular Biology, The Plant Signaling Mechanisms Laboratory, University of Lausanne, Lausanne, Switzerland
| | - Caroline Broyart
- Department of Plant Molecular Biology, The Plant Signaling Mechanisms Laboratory, University of Lausanne, Lausanne, Switzerland
| | - Daria Balcerowicz
- Department of Biology, Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
| | - Hamada AbdElgawad
- Department of Biology, Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Andrea Bassi
- Department of Physics, Politecnico di Milano, Milan, Italy
| | - Daniel Santa Cruz Damineli
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
- Center for Mathematics, Computing and Cognition, Federal University of ABC, Santo André, Brazil
| | - Alex Costa
- Department of Biosciences, University of Milan, Milan, Italy
- Institute of Biophysics, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - José A Feijó
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | | | | | | | - Julia Santiago
- Department of Plant Molecular Biology, The Plant Signaling Mechanisms Laboratory, University of Lausanne, Lausanne, Switzerland.
| | - Herman Höfte
- Institut Jean-Pierre Bourgin, AgroParisTech, Université Paris-Saclay, Versailles, France.
| | - Kris Vissenberg
- Department of Biology, Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium.
- Department of Agriculture, Plant Biochemistry and Biotechnology Lab, Hellenic Mediterranean University, Heraklion, Greece.
| |
Collapse
|
34
|
Long Q, Wei M, Wang Y, Pang F. Design of a multi-epitope vaccine against goatpox virus using an immunoinformatics approach. Front Cell Infect Microbiol 2024; 13:1309096. [PMID: 38487680 PMCID: PMC10937444 DOI: 10.3389/fcimb.2023.1309096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/22/2023] [Indexed: 03/17/2024] Open
Abstract
Introduction Goatpox, a severe infectious disease caused by goatpox virus (GTPV), leads to enormous economic losses in the livestock industry. Traditional live attenuated vaccines cause serious side effects and exist a risk of dispersal. Therefore, it is urgent to develop efficient and safer vaccines to prevent and control of GTPV. Methods In the present study, we are aimed to design a multi-epitope subunit vaccine against GTPV using an immunoinformatics approach. Various immunodominant cytotoxic T lymphocytes (CTL) epitopes, helper T lymphocytes (HTL) epitopes, and B-cell epitopes from P32, L1R, and 095 proteins of GTPV were screened and liked by the AAY, GPGPG, and KK connectors, respectively. Furthermore, an adjuvant β-defensin was attached to the vaccine's N-terminal using the EAAAK linker to enhance immunogenicity. Results The constructed vaccine was soluble, non-allergenic and non-toxic and exhibited high levels of antigenicity and immunogenicity. The vaccine's 3D structure was subsequently predicted, refined and validated, resulting in an optimized model with a Z-value of -3.4. Molecular docking results demonstrated that the vaccine had strong binding affinity with TLR2(-27.25 kcal/mol), TLR3(-39.84 kcal/mol), and TLR4(-59.42 kcal/mol). Molecular dynamics simulation results indicated that docked vaccine-TLR complexes were stable. Immune simulation analysis suggested that the vaccine can induce remarkable increase in antibody titers of IgG and IgM, higher levels of IFN-γ and IL-2. Conclusion The designed GTPV multi-epitope vaccine is structurally stable and can induce robust humoral and cellular immune responses, which may be a promising vaccine candidate against GTPV.
Collapse
Affiliation(s)
| | | | | | - Feng Pang
- Department of Veterinary Medicine, College of Animal Science, Guizhou University, Guiyang, China
| |
Collapse
|
35
|
Zhang TY, Chen YQ, Tan JC, Zhou JA, Chen WN, Jiang T, Zha JY, Zeng XK, Li BW, Wei LQ, Zou Y, Zhang LY, Hong YM, Wang XL, Zhu RZ, Xu WX, Xi J, Wang QQ, Pan L, Zhang J, Luan Y, Zhu RX, Wang H, Chen C, Liu NN. Global fungal-host interactome mapping identifies host targets of candidalysin. Nat Commun 2024; 15:1757. [PMID: 38413612 PMCID: PMC10899660 DOI: 10.1038/s41467-024-46141-x] [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: 07/03/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Candidalysin, a cytolytic peptide toxin secreted by the human fungal pathogen Candida albicans, is critical for fungal pathogenesis. Yet, its intracellular targets have not been extensively mapped. Here, we performed a high-throughput enhanced yeast two-hybrid (HT-eY2H) screen to map the interactome of all eight Ece1 peptides with their direct human protein targets and identified a list of potential interacting proteins, some of which were shared between the peptides. CCNH, a regulatory subunit of the CDK-activating kinase (CAK) complex involved in DNA damage repair, was identified as one of the host targets of candidalysin. Mechanistic studies revealed that candidalysin triggers a significantly increased double-strand DNA breaks (DSBs), as evidenced by the formation of γ-H2AX foci and colocalization of CCNH and γ-H2AX. Importantly, candidalysin binds directly to CCNH to activate CAK to inhibit DNA damage repair pathway. Loss of CCNH alleviates DSBs formation under candidalysin treatment. Depletion of candidalysin-encoding gene fails to induce DSBs and stimulates CCNH upregulation in a murine model of oropharyngeal candidiasis. Collectively, our study reveals that a secreted fungal toxin acts to hijack the canonical DNA damage repair pathway by targeting CCNH and to promote fungal infection.
Collapse
Affiliation(s)
- Tian-Yi Zhang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yao-Qi Chen
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing-Cong Tan
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jin-An Zhou
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wan-Ning Chen
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Tong Jiang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jin-Yin Zha
- State Key Laboratory of Systems Medicine for Cancer, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Xiang-Kang Zeng
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Science, Shanghai, China
| | - Bo-Wen Li
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lu-Qi Wei
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yun Zou
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lu-Yao Zhang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yue-Mei Hong
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiu-Li Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Run-Ze Zhu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wan-Xing Xu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Xi
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qin-Qin Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lei Pan
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Science, Shanghai, China
| | - Jian Zhang
- State Key Laboratory of Systems Medicine for Cancer, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Yang Luan
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Rui-Xin Zhu
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Changbin Chen
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Ning-Ning Liu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| |
Collapse
|
36
|
Munna MMR, Islam MA, Shanta SS, Monty MA. Structural, functional, molecular docking analysis of a hypothetical protein from Talaromyces marneffei and its molecular dynamic simulation: an in-silico approach. J Biomol Struct Dyn 2024:1-20. [PMID: 38345137 DOI: 10.1080/07391102.2024.2314264] [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: 07/31/2023] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
Telaromyces marneffei (formerly Penicillium marneffei) is an endemic pathogenic fungus in Southern China and Southeast Asia. It can cause disease in patients with travel-related exposure to this organism and high morbidity and mortality in acquired immune deficiency syndrome (AIDS). In this study, we analyzed the structure and function of a hypothetical protein from T. marneffei using several bioinformatics tools and servers to unveil novel pharmacological targets and design a peptide vaccine against specific epitopes. A total of seven functional epitopes were screened on the protein, and 'STGVDMWSV' was the most antigenic, non-allergenic and non-toxic. Molecular docking showed stronger affinity between the CTL epitope 'STGVDMWSV' and the MHC I allele HLA-A*02:01, a higher docking score -234.98 kcal/mol, revealed stable interactions during a 100 ns molecular dynamic simulation. Overall, the results of this study revealed that this hypothetical protein is crucial for comprehending biochemical, physiological pathways and identifying novel therapeutic targets for human health. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Md Masudur Rahman Munna
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Ariful Islam
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, PR China
| | - Saima Sajnin Shanta
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Masuma Akter Monty
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, PR China
| |
Collapse
|
37
|
Verma AK, Srivastava SK. In silico and structural investigation of sulfonamides targeting VraSR two component system in methicillin-resistant Staphylococcus aureus. J Biomol Struct Dyn 2024:1-21. [PMID: 38319034 DOI: 10.1080/07391102.2024.2309679] [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: 10/03/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Drug-resistant Staphylococcus aureus strains are global health concerns. Several studies have shown that these strains can develop defences against cell wall antibiotics such as β-lactams, glycopeptides and daptomycin which target cell wall biosynthesis. The coordination of these responses have been associated with two component system (TCS) regulated by histidine kinase protein (VraS) and its cognate regulator VraR which influences the target DNA upon signal recognition. Computer-based screening methods, predictions and simulations have emerged as more efficient and quick ways to identify promising new compound leads from large databases against emerging drug targets thus allowing prediction of small select set of molecules for further validations. These combined approaches conserve valuable time and resources. Due to methicillin resistance, sulfonamide-derivative medications have been found to be effective treatment strategy to treat S. aureus infections. The current study used ligand-based virtual screening (LBVS) to identify powerful sulfonamide derivative inhibitors from an antibacterial compound library against VraSR signaling components, VraS and VraR. We identified promising sulfonamide derivative [compound 5: (4-[(1-{[(3,5-Dimethoxyphenyl)Carbamoyl]Methyl}-2,4-Dioxo-1,2,3,4-Tetrahydroquinazolin-3-Yl)Methyl]-N-[(Furan-2-Yl)Methyl]Benzamide)] with reasonable binding parameters of -31.38 kJ/mol and ΔGbind score of -294.32 kJ/mol against ATP binding domain of sensor kinase VraS. We further identified four compounds N1 (PCID83276726), N3 (PCID83276757), N9 (PCID3672584), and N10 (PCID20900589) against VraR DNA binding domain (VraRC) with ΔGbind energies of -190.27, -237.54, -165.21, and -190.88 kJ/mol, respectively. Structural and simulation analyses further suggest their stable interactions with DNA interacting residues and potential to disrupt DNA binding domain dimerization; therefore, it is prudent to further investigate and characterize them as VraR dimer disruptors and inhibit other promoter binding site. Interestingly, the discovery of drugs that target VraS and VraR may open new therapeutic avenues for drug-resistant S. aureus. These predictions based on screening, simulations and binding affinities against VraSR components hold promise for opening novel therapeutic avenues against drug-resistant S. aureus and present opportunities for repositioning efforts. These efforts aim to create analogs with enhanced potency and selectivity against two-component signaling systems that significantly contribute to virulence in MRSA or VRSA. These analyses contribute valuable insights into potential avenues for combating antibiotic-resistant S. aureus through computationally driven drug discovery strategies.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abhishek Kumar Verma
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Sandeep Kumar Srivastava
- Structural Biology & Bioinformatics Laboratory, Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| |
Collapse
|
38
|
Fan M, Zhou Z, Zhu W, Li M, Tu Y, Yu Z, Li J, Zhang M, Liang K. Reinforced dentin remineralization via a novel dual-affinity peptide. Dent Mater 2024; 40:254-266. [PMID: 37989605 DOI: 10.1016/j.dental.2023.11.009] [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: 07/25/2023] [Revised: 10/30/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023]
Abstract
OBJECTIVES In light of the constantly flowing saliva, anti-caries remineralization agents are inclined to be taken away. Owing to their limited residence time, the remineralization effect is not as desirable as expected. Hence, our study aimed to synthesize a novel peptide (DGP) with high affinity to both collagen fibrils and hydroxyapatite, and investigated its dentin remineralization efficacy in vitro and anti-caries capability in vivo. METHODS DGP was synthesized through Fmoc solid-phase reaction. The binding ability and interaction mechanism of DGP to demineralized dentin were investigated. Dentin specimens were demineralized, then treated with DGP and deionized water respectively. The specimens were incubated in artificial saliva and in-vitro remineralization effectiveness was analyzed after 14 days. The rat caries model was established to further scrutinize the in-vivo efficacy of caries prevention. RESULTS DGP possesses an enhanced adhesion force of 12.29 ± 1.12 nN to demineralized dentin. The favorable adsorption capacity is ascribed to the stable hydrogen bonds between S2P-101 and ASP-100 of DGP and GLY33 and PRO-16 of collagen fibers. Abundant mineral deposits and remarkable tubule occlusion were observed in the DGP group. DGP-treated dentin obtained notable microhardness recovery and higher mineral content after a 14-day remineralization regimen. DGP also demonstrated potent caries prevention in vivo, with substantially fewer carious lesions and significantly lower Keyes scoring. SIGNIFICANCE DGP proves to possess a high affinity to demineralized dentin regardless of saliva flowing, thus enhancing remineralization potency significantly in vitro and in vivo, potential for dental caries prevention and combatting initial dentin caries clinically.
Collapse
Affiliation(s)
- Menglin Fan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zilin Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Wanchun Zhu
- Chongqing Medical University Stomatology College, Chongqing 401147, China
| | - Meng Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Yuanyuan Tu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Zhaohan Yu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Min Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Kunneng Liang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
39
|
Wang Y, Wu A, Xu Z, Zhang H, Li H, Fu S, Liu Y, Cui L, Miao Y, Wang Y, Zhumanov K, Xu Y, Sheng J, Yi J, Chen C. A multi-epitope subunit vaccine based on CU/ZN-SOD, OMP31 and BP26 against Brucella melitensis infection in BALB/C mice. Int Immunopharmacol 2024; 127:111351. [PMID: 38113688 DOI: 10.1016/j.intimp.2023.111351] [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: 10/09/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
Brucellosis, a zoonosis caused by Brucella, is highly detrimental to both humans and animals. Most existing vaccines are live attenuated vaccines with safety flaws for people and animals. Therefore, it is advantageous to design a multi-epitope subunit vaccine (MEV) to prevent Brucella infection. To this end, we applied a reverse vaccinology approach. Six cytotoxic T cell (CTL) epitopes, seven T helper cell (HTL) epitopes, and four linear B cell epitopes from CU/ZN-SOD, Omp31, and BP26 were obtained. We linked the CTL, HTL, B-cell epitopes, the appropriate CTB molecular adjuvant, and the universal T helper lymphocyte epitope, PADRE, with linkers AAY, GPPGG, and KK, respectively. This yielded a 412-amino acid MEV construct, which we named MEVcob. The immunogenicity, stability, safety, and feasibility of the construct were evaluated by bioinformatics tools (including the AlphaFold2 prediction tool, the AlphaFold2 tool, NetMHC-I pan 4.0 server, IEDB MHC-I server, ABCpred service, and C-ImmSim server); the physicochemical properties, secondary and tertiary structures, and binding ability of MEVocb to toll-like receptor 4 (TLR4) was analyzed. Then, codon adaptation and computer cloning studies were performed. MEVocb is highly immunogenic in immunostimulation experiments, The proteins translated by these sequences were relatively stable, exhibiting a high antigenic index. Furthermore, mouse experiments confirmed that the MEVocb construct could raise IFN-γ, IgG, IgG2a, IgG1, IL-2, TNF-α levels in mice, indicating that induced a specific humoral and cellular immune response in BALB/c mice. This vaccine induced a statistically significant level of protection in BALB/c mice when challenged with Brucella melitensis 043 in Xinjiang. Briefly, we utilized immunoinformatic tools to design a novel multi-epitope subunit candidate vaccine against Brucella. This vaccine aims to induce host immune responses and confer specific protective effects. The study results offer a theoretical foundation for the development of a novel Brucella subunit vaccine.
Collapse
Affiliation(s)
- Yueli Wang
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China
| | - Aodi Wu
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China
| | - Zhenyu Xu
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China
| | - Huan Zhang
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China
| | - Honghuan Li
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China
| | - Shuangshuang Fu
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China
| | - Yajing Liu
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China
| | - Lijin Cui
- Fujian Biotechnology Co., LTD., 353000 Nanping, Fujian, China
| | - Yuhe Miao
- Fujian Biotechnology Co., LTD., 353000 Nanping, Fujian, China
| | - Yong Wang
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China
| | - Kaiat Zhumanov
- Kazakh National Agrarian University, The Republic of Kazakhstan
| | - Yimei Xu
- Xinjiang Center for Disease Control and Prevention, 830000 Urumqi, Xinjiang, China
| | - Jinliang Sheng
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China.
| | - Jihai Yi
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China.
| | - Chuangfu Chen
- School of Animal Science and Technology, Shihezi University, 832000 Shihezi City, Xinjiang, China.
| |
Collapse
|
40
|
Rosilan NF, Jamali MAM, Sufira SA, Waiho K, Fazhan H, Ismail N, Sung YY, Mohamed-Hussein ZA, Hamid AAA, Afiqah-Aleng N. Molecular docking and dynamics simulation studies uncover the host-pathogen protein-protein interactions in Penaeus vannamei and Vibrio parahaemolyticus. PLoS One 2024; 19:e0297759. [PMID: 38266027 PMCID: PMC10807825 DOI: 10.1371/journal.pone.0297759] [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: 08/03/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024] Open
Abstract
Shrimp aquaculture contributes significantly to global economic growth, and the whiteleg shrimp, Penaeus vannamei, is a leading species in this industry. However, Vibrio parahaemolyticus infection poses a major challenge in ensuring the success of P. vannamei aquaculture. Despite its significance in this industry, the biological knowledge of its pathogenesis remains unclear. Hence, this study was conducted to identify the interaction sites and binding affinity between several immune-related proteins of P. vannamei with V. parahaemolyticus proteins associated with virulence factors. Potential interaction sites and the binding affinity between host and pathogen proteins were identified using molecular docking and dynamics (MD) simulation. The P. vannamei-V. parahaemolyticus protein-protein interaction of Complex 1 (Ferritin-HrpE/YscL family type III secretion apparatus protein), Complex 2 (Protein kinase domain-containing protein-Chemotaxis CheY protein), and Complex 3 (GPCR-Chemotaxis CheY protein) was found to interact with -4319.76, -5271.39, and -4725.57 of the docked score and the formation of intermolecular bonds at several interacting residues. The docked scores of Complex 1, Complex 2, and Complex 3 were validated using MD simulation analysis, which revealed these complexes greatly contribute to the interactions between P. vannamei and V. parahaemolyticus proteins, with binding free energies of -22.50 kJ/mol, -30.20 kJ/mol, and -26.27 kJ/mol, respectively. This finding illustrates the capability of computational approaches to search for molecular binding sites between host and pathogen, which could increase the knowledge of Vibrio spp. infection on shrimps, which then can be used to assist in the development of effective treatment.
Collapse
Affiliation(s)
- Nur Fathiah Rosilan
- Institute of Climate Adaptation and Marine Biotechnology (ICAMB), Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Muhamad Arif Mohamad Jamali
- Faculty of Science and Technology, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Nilai, Negeri Sembilan, Malaysia
| | - Siti Aishah Sufira
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kuliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, Kuantan, Pahang, Malaysia
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Hanafiah Fazhan
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Noraznawati Ismail
- Institute of Climate Adaptation and Marine Biotechnology (ICAMB), Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Yeong Yik Sung
- Institute of Climate Adaptation and Marine Biotechnology (ICAMB), Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- UKM Medical Molecular Biology Institute, UKM Medical Centre, Jalan Yaacob Latiff, Cheras, Kuala Lumpur, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kuliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, Kuantan, Pahang, Malaysia
| | - Nor Afiqah-Aleng
- Institute of Climate Adaptation and Marine Biotechnology (ICAMB), Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| |
Collapse
|
41
|
Gonzalez JJI, Hossain MF, Neef J, Zwack EE, Tsai CM, Raafat D, Fechtner K, Herzog L, Kohler TP, Schlüter R, Reder A, Holtfreter S, Liu GY, Hammerschmidt S, Völker U, Torres VJ, van Dijl JM, Lillig CH, Bröker BM, Darisipudi MN. TLR4 sensing of IsdB of Staphylococcus aureus induces a proinflammatory cytokine response via the NLRP3-caspase-1 inflammasome cascade. mBio 2024; 15:e0022523. [PMID: 38112465 PMCID: PMC10790753 DOI: 10.1128/mbio.00225-23] [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: 01/27/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE The prevalence of multidrug-resistant Staphylococcus aureus is of global concern, and vaccines are urgently needed. The iron-regulated surface determinant protein B (IsdB) of S. aureus was investigated as a vaccine candidate because of its essential role in bacterial iron acquisition but failed in clinical trials despite strong immunogenicity. Here, we reveal an unexpected second function for IsdB in pathogen-host interaction: the bacterial fitness factor IsdB triggers a strong inflammatory response in innate immune cells via Toll-like receptor 4 and the inflammasome, thus acting as a novel pathogen-associated molecular pattern of S. aureus. Our discovery contributes to a better understanding of how S. aureus modulates the immune response, which is necessary for vaccine development against the sophisticated pathogen.
Collapse
Affiliation(s)
| | - Md Faruq Hossain
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Jolanda Neef
- Department of Medical Microbiology, University of Groningen, University Medical Center, Groningen, the Netherlands
| | - Erin E. Zwack
- Department of Microbiology, New York University Grossman School of Medicine, New York, USA
| | - Chih-Ming Tsai
- Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California, USA
| | - Dina Raafat
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Kevin Fechtner
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Luise Herzog
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Thomas P. Kohler
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Alexander Reder
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Silva Holtfreter
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - George Y. Liu
- Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California, USA
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, USA
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center, Groningen, the Netherlands
| | - Christopher H. Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Barbara M. Bröker
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Murty N. Darisipudi
- Institute of Immunology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
42
|
Khatua S, Roy A, Sen P, Ray S. Elucidation of the structural dynamics of mutations in PHB2 protein associated with growth suppression and cancer progression. Gene 2024; 890:147820. [PMID: 37739195 DOI: 10.1016/j.gene.2023.147820] [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: 07/16/2023] [Revised: 09/03/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Prohibitin is a multifunctional protein that plays an important role in numerous cellular processes. Membrane-associated mitochondrial prohibitin complex is made up of two subunits, PHB1 and PHB2 which are ubiquitously expressed and analogous to each other. High levels of prohibitin expression have consequently been found in esophageal cancer, endometrial adenocarcinoma, gastric cancer, hepatocellular carcinoma, breast cancer and bladder cancer. The aim of this study is to analyse two-point mutation PHB2_MT1(I → A) and PHB2_MT2(I → P), their effect on PHB2 protein and its effect on formation of mitochondrial complex. It is a residual level study, based on current experimental validation. To establish the effects of the two-point mutations, computational approaches such as molecular modelling, molecular docking, normal mode simulation, molecular dynamics simulations and MM/GBSA were used. An analysis of the energy dynamics of both unbound and complex proteins was conducted to elucidate how mutations impact the energy distribution of PHB2. Our study confirmed that the two mutations decreased the overall stability of PHB2. This was evidenced by heightened atomic fluctuations within the mutated region, accompanied by elevated deviations observed in RMSD and Rg values. Furthermore, these mutations were correlated with a decline in the organization of secondary structural elements. The mutations in PHB2_MT1 and PHB2_MT2 resulted in formation a less stable prohibitin complex. Thus, PHB1 and PHB2 may act as molecular target or novel biomarkers for therapeutic intervention in numerous forms of malignancies.
Collapse
Affiliation(s)
- Susmita Khatua
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Pritha Sen
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India.
| |
Collapse
|
43
|
Marques PH, Tiwari S, Felice AG, Jaiswal AK, Aburjaile FF, Azevedo V, Silva-Vergara ML, Ferreira-Paim K, Soares SDC, Fonseca FM. Design of a Multi-Epitope Vaccine against Histoplasma capsulatum through Immunoinformatics Approaches. J Fungi (Basel) 2024; 10:43. [PMID: 38248954 PMCID: PMC10817582 DOI: 10.3390/jof10010043] [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: 10/25/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
Histoplasmosis is a widespread systemic disease caused by Histoplasma capsulatum, prevalent in the Americas. Despite its significant morbidity and mortality rates, no vaccines are currently available. Previously, five vaccine targets and specific epitopes for H. capsulatum were identified. Immunoinformatics has emerged as a novel approach for determining the main immunogenic components of antigens through in silico methods. Therefore, we predicted the main helper and cytotoxic T lymphocytes and B-cell epitopes for these targets to create a potential multi-epitope vaccine known as HistoVAC-TSFM. A total of 38 epitopes were found: 23 common to CTL and B-cell responses, 11 linked to HTL and B cells, and 4 previously validated epitopes associated with the B subunit of cholera toxin, a potent adjuvant. In silico evaluations confirmed the stability, non-toxicity, non-allergenicity, and non-homology of these vaccines with the host. Notably, the vaccine exhibited the potential to trigger both innate and adaptive immune responses, likely involving the TLR4 pathway, as supported by 3D modeling and molecular docking. The designed HistoVAC-TSFM appears promising against Histoplasma, with the ability to induce important cytokines, such as IFN-γ, TNF-α, IL17, and IL6. Future studies could be carried out to test the vaccine's efficacy in in vivo models.
Collapse
Affiliation(s)
- Pedro Henrique Marques
- Postgraduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (P.H.M.); (A.K.J.)
- Department of Preventive Veterinary, Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | - Sandeep Tiwari
- Institute of Biology, Federal University of Bahia, Salvador 40170-115, Brazil;
- Institute of Health Sciences, Federal University of Bahia, Salvador 40170-115, Brazil
| | - Andrei Giacchetto Felice
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (A.G.F.); (S.d.C.S.)
| | - Arun Kumar Jaiswal
- Postgraduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (P.H.M.); (A.K.J.)
| | - Flávia Figueira Aburjaile
- Department of Preventive Veterinary, Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | - Mario León Silva-Vergara
- Department of Infectious Diseases, Federal University of Triangulo Mineiro, Uberaba 38025-440, Brazil;
| | - Kennio Ferreira-Paim
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (A.G.F.); (S.d.C.S.)
| | - Siomar de Castro Soares
- Department of Microbiology, Immunology and Parasitology, Federal University of Triangulo Mineiro, Uberaba 38015-050, Brazil; (A.G.F.); (S.d.C.S.)
| | | |
Collapse
|
44
|
Saini S, Kumar Y. Structural and functional analysis of engineered antibodies for cancer immunotherapy: insights into protein compactness and solvent accessibility. J Biomol Struct Dyn 2024:1-14. [PMID: 38173178 DOI: 10.1080/07391102.2023.2300129] [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: 08/14/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Antibodies are crucial tools in various biomedical applications, including immunotherapy. In this study, we focused on designing and engineering antibodies to enhance their structural dynamics and functional properties. By employing advanced computational techniques and experimental validation, we gained crucial insights into the impact of specific mutations on the engineered antibodies. This study investigates the design and engineering of antibodies to improve their structural dynamics and functional properties. Structural attributes, such as protein compactness and solvent accessibility, were assessed, revealing interesting trends in anti-CD3 and anti-HER2 antibodies. Mutations in CD3 antibodies resulted in a more stable conformation, while mutant HER2 antibodies exhibited altered interaction with the target. Analysis of secondary structure assignments demonstrated significant changes in the folding and stability of the mutant antibodies compared to the wild-type counterparts. The conformational landscape of the engineered antibodies was explored, providing insights into folding pathways and binding mechanisms. Overall, the current study highlights the significance of antibody design and engineering in modulating structural dynamics and functional properties. The findings contribute to developing improved immunotherapeutic strategies by optimising antibody-based therapeutics for targeted diseases with enhanced efficacy and precision.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Samvedna Saini
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
| | - Yatender Kumar
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
| |
Collapse
|
45
|
Patel KN, Chavda D, Manna M. Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies. Methods Mol Biol 2024; 2780:165-201. [PMID: 38987470 DOI: 10.1007/978-1-0716-3985-6_11] [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] [Indexed: 07/12/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a novel class of proteins that have established a significant importance and attention within a very short period of time. These proteins are essentially characterized by their inherent structural disorder, encoded mainly by their amino acid sequences. The profound abundance of IDPs and intrinsically disordered regions (IDRs) in the biological world delineates their deep-rooted functionality. IDPs and IDRs convey such extensive functionality through their unique dynamic nature, which enables them to carry out huge number of multifaceted biomolecular interactions and make them "interaction hub" of the cellular systems. Additionally, with such widespread functions, their misfunctioning is also intimately associated with multiple diseases. Thus, understanding the dynamic heterogeneity of various IDPs along with their interactions with respective binding partners is an important field with immense potentials in biomolecular research. In this context, molecular docking-based computational approaches have proven to be remarkable in case of ordered proteins. Molecular docking methods essentially model the biomolecular interactions in both structural and energetic terms and use this information to characterize the putative interactions between the two participant molecules. However, direct applications of the conventional docking methods to study IDPs are largely limited by their structural heterogeneity and demands for unique IDP-centric strategies. Thus, in this chapter, we have presented an overview of current methodologies for successful docking operations involving IDPs and IDRs. These specialized methods majorly include the ensemble-based and fragment-based approaches with their own benefits and limitations. More recently, artificial intelligence and machine learning-assisted approaches are also used to significantly reduce the complexity and computational burden associated with various docking applications. Thus, this chapter aims to provide a comprehensive summary of major challenges and recent advancements of molecular docking approaches in the IDP field for their better utilization and greater applicability.Asp (D).
Collapse
Affiliation(s)
- Keyur N Patel
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Dhruvil Chavda
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Moutusi Manna
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
| |
Collapse
|
46
|
Gabrani R, Jain P, Sharma S, Ghildiyal R, Prakash V. From Multiple Protein Docking to Protein-Protein Docking at Interactome Level. Methods Mol Biol 2024; 2780:69-89. [PMID: 38987464 DOI: 10.1007/978-1-0716-3985-6_5] [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] [Indexed: 07/12/2024]
Abstract
Molecular docking is used to anticipate the optimal orientation of a particular molecule to a target to form a stable complex. It makes predictions about the 3D structure of any complex based on the binding characteristics of the ligand and the target receptor usually a protein. It is an exceptionally useful tool, which is used as a model to study how ligands attach to proteins. Docking can also be used for studying the interaction of ligands and proteins to analyze inhibitory efficacy. The ligand may also be a protein, making it possible to study interactions between two different proteins using the numerous docking tools available for basic research on protein interactions. The protein-protein docking is a crucial approach to understanding the protein interactions and predicting the structure of protein complexes that have not yet been experimentally determined. Moreover, the protein-protein interactions can predict the function of target proteins and the drug-like properties of molecules. Therefore, protein docking assists in uncovering insights into protein interactions and also aids in a better understanding of molecular pathways/mechanisms. This chapter comprehends the various tools for protein-protein docking (pairwise and multiple), including their methodologies and analysis of output as results.
Collapse
Affiliation(s)
- Reema Gabrani
- Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India.
| | - Priyanjal Jain
- Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Srishti Sharma
- Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Ritu Ghildiyal
- Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - Vijeta Prakash
- Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| |
Collapse
|
47
|
Zhang P, Wang K, Hu T, Xu M, You X, Chen M, Tang X, Hu H, Jiang Y, Zhao W, Tan S. A novel fully human anti-NT-ANGPTL3 antibody from phage display library exhibits potent ApoB, TG, and LDL-C lowering activities in hyperlipidemia mice. FASEB J 2024; 38:e23399. [PMID: 38174870 DOI: 10.1096/fj.202301564rr] [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: 08/02/2023] [Revised: 12/06/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
Dyslipidemia is characterized by elevated plasma levels of low-density lipoprotein cholesterol (LDL-C), triglycerides (TG), and TG-rich lipoprotein (TGRLs) in circulation, and is closely associated with the incidence and development of cardiovascular disease. Angiopoietin-like protein 3 (ANGPTL3) deficiency has been identified as a cause of familial combined hypolipidemia in humans, which allows it to be an important therapeutic target for reducing plasma lipids. Here, we report the discovery and characterization of a novel fully human antibody F1519-D95aA against N-terminal ANGPTL3 (NT-ANGPTL3), which potently inhibits NT-ANGPTL3 with a KD as low as 9.21 nM. In hyperlipidemic mice, F1519-D95aA shows higher apolipoprotein B (ApoB) and TG-lowering, and similar LDL-C reducing activity as compared to positive control Evinacumab (56.50% vs 26.01% decrease in serum ApoB levels, 30.84% vs 25.28% decrease in serum TG levels, 23.32% vs 22.52% decrease in serum LDLC levels, relative to vehicle group). Molecular docking and binding energy calculations reveal that the F1519-D95aA-ANGPTL3 complex (10 hydrogen bonds, -65.51 kcal/mol) is more stable than the Evinacumab-ANGPTL3 complex (4 hydrogen bonds, -63.76 kcal/mol). Importantly, F1519-D95aA binds to ANGPTL3 with different residues in ANGPTL3 from Evinacumab, suggesting that F1519-D95aA may be useful for the treatment of patients resistant to Evinacumab. In conclusion, F1519-D95aA is a novel fully human anti-NT-ANGPTL3 antibody with potent plasma ApoB, TG, and LDL-C lowering activities, which can potentially serve as a therapeutic agent for hyperlipidemia and relevant cardiovascular diseases.
Collapse
Affiliation(s)
- Panpan Zhang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Ke Wang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Tuo Hu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Menglong Xu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Xiangyan You
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Manman Chen
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Xuan Tang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Huajing Hu
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Yiwei Jiang
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Wenfeng Zhao
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| | - Shuhua Tan
- Department of Cell and Molecular Biology, School of Life Science and Technology, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, PR China
| |
Collapse
|
48
|
Kumar P, Kumar P, Shrivastava A, Dar MA, Lokhande KB, Singh N, Singh A, Velayutham R, Mandal D. Immunoinformatics-based multi-epitope containing fused polypeptide vaccine design against visceral leishmaniasis with high immunogenicity and TLR binding. Int J Biol Macromol 2023; 253:127567. [PMID: 37866569 DOI: 10.1016/j.ijbiomac.2023.127567] [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: 07/24/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
Visceral leishmaniasis (VL) is the most lethal among all leishmaniasis diseases and remains categorized as a neglected tropical disease (NTD). This study aimed to develop a peptide-based multi-epitope vaccine construct against VL using immunoinformatics methodologies. To achieve this, four distinct proteins were screened to identify peptides consisting of 9-15 amino acids with high binding affinity to toll-like receptors (TLRs), strong antigenicity, low allergenicity, and minimal toxicity. The resulting multi-epitope vaccine construct was fused in a tandem arrangement with appropriate linker peptides and exhibited superior properties related to cytotoxic T lymphocytes (CTLs), helper T lymphocytes (HTLs), and B-cell epitopes. Subsequently, a three-dimensional (3D) model of the vaccine construct was generated, refined, and validated for structural stability and immune response capabilities. Molecular docking and simulations confirmed the vaccine construct's stability and binding affinities with TLRs, with TLR4 displaying the highest binding affinity, followed by TLR2 and TLR3. Additionally, simulations predicted robust cellular and humoral antibody-mediated immune responses elicited by the designed vaccine construct. Notably, this vaccine construct includes proteins from various pathways of Leishmania donovani (LD), which have not been previously utilized in VL vaccine design. Thus, this study opens new avenues for the development of vaccines against diverse protozoan diseases.
Collapse
Affiliation(s)
- Pawan Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) Hajipur-Vaishali, Bihar 844102, India
| | - Prakash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) Hajipur-Vaishali, Bihar 844102, India
| | - Ashish Shrivastava
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Mukhtar Ahmad Dar
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER) Hajipur-Vaishali, Bihar 844102, India
| | - Kiran Bharat Lokhande
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Nidhi Singh
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) Ahmedabad, India
| | - Ashutosh Singh
- Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, UP, India
| | - Ravichandiran Velayutham
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) Hajipur-Vaishali, Bihar 844102, India; National Institute of Pharmaceutical Education and Research (NIPER) Kolkata, India
| | - Debabrata Mandal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER) Hajipur-Vaishali, Bihar 844102, India.
| |
Collapse
|
49
|
Marques PH, Rodrigues TCV, Santos EH, Bleicher L, Aburjaile FF, Martins FS, Oliveira CJF, Azevedo V, Tiwari S, Soares S. Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches. J Biomol Struct Dyn 2023:1-16. [PMID: 38112302 DOI: 10.1080/07391102.2023.2293256] [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: 02/08/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Pedro Henrique Marques
- Institute of Biological Sciences, Post-graduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thais Cristina Vilela Rodrigues
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eduardo Horta Santos
- Institute of Biological Sciences, Post-graduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flavia Figueira Aburjaile
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flaviano S Martins
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlo Jose Freire Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Siomar Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| |
Collapse
|
50
|
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571185. [PMID: 38168257 PMCID: PMC10760024 DOI: 10.1101/2023.12.11.571185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In this study, we combined AI-based atomistic structural modeling and microsecond molecular simulations of the SARS-CoV-2 Spike complexes with the host receptor ACE2 for XBB.1.5+L455F, XBB.1.5+F456L(EG.5) and XBB.1.5+L455F/F456L (FLip) lineages to examine the mechanisms underlying the role of convergent evolution hotspots in balancing ACE2 binding and antibody evasion. Using the ensemble-based mutational scanning of the spike protein residues and physics-based rigorous computations of binding affinities, we identified binding energy hotspots and characterized molecular basis underlying epistatic couplings between convergent mutational hotspots. Consistent with the experiments, the results revealed the mediating role of Q493 hotspot in synchronization of epistatic couplings between L455F and F456L mutations providing a quantitative insight into the mechanism underlying differences between XBB lineages. Mutational profiling is combined with network-based model of epistatic couplings showing that the Q493, L455 and F456 sites mediate stable communities at the binding interface with ACE2 and can serve as stable mediators of non-additive couplings. Structure-based mutational analysis of Spike protein binding with the class 1 antibodies quantified the critical role of F456L and F486P mutations in eliciting strong immune evasion response. The results of this analysis support a mechanism in which the emergence of EG.5 and FLip variants may have been dictated by leveraging strong epistatic effects between several convergent revolutionary hotspots that provide synergy between the improved ACE2 binding and broad neutralization resistance. This interpretation is consistent with the notion that functionally balanced substitutions which simultaneously optimize immune evasion and high ACE2 affinity may continue to emerge through lineages with beneficial pair or triplet combinations of RBD mutations involving mediators of epistatic couplings and sites in highly adaptable RBD regions.
Collapse
|