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Bialves TS, Bastos LL, Parra JAA, Moysés MN, Marques E, de Castro Pimenta AM, Quintela FM, Mariano DCB, Carvalho FC, de Melo-Minardi RC, Boyle RT. Interaction of DisBa01 peptide from Bothrops alternatus venom with BRAF melanoma receptors: Modeling and molecular docking. Int J Biol Macromol 2024; 274:133283. [PMID: 38909731 DOI: 10.1016/j.ijbiomac.2024.133283] [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: 01/09/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 06/25/2024]
Abstract
Metastatic melanoma is highly aggressive and challenging, often leading to a grim prognosis. Its progression is swift, especially when mutations like BRAFV600E continuously activate pathways vital for cell growth and survival. Although several treatments target this mutation, resistance typically emerges over time. In recent decades, research has underscored the potential of snake venoms and peptides as bioactive substances for innovative drugs, including anti-coagulants, anti-microbial, and anti-cancer agents. Leveraging this knowledge, we propose employing a bioinformatics simulation approach to: a) Predict how well a peptide (DisBa01) from Bothrops alternatus snake venom binds to the melanoma receptor BRAFV600E via Molecular Docking. b) Identify the specific peptide binding sites on receptors and analyze their proximity to active receptor sites. c) Evaluate the behavior of resulting complexes through molecular dynamics simulations. d) Assess whether this peptide qualifies as a candidate for anti-melanoma therapy. Our findings reveal that DisBa01 enhances stability in the BRAFV600E melanoma receptor structure by binding to its RGD motif, an interaction absent in the BRAF WT model. Consequently, both docking and molecular dynamics simulations suggest that DisBa01 shows promise as a BRAFV600E inhibitor.
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Affiliation(s)
- Tatiane Senna Bialves
- Graduate Program in Physiological Sciences (PPGCF), Federal University of Rio Grande - FURG, Av. Italy, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil.
| | - Luana Luiza Bastos
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - John Alexanders Amaya Parra
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maurício Nogueira Moysés
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edleusa Marques
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Adriano Monteiro de Castro Pimenta
- Graduate Program in Biochemistry and Immunology, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernando Marques Quintela
- Instituto Nacional de Pesquisas do Pantanal- Museu Paraense Emílio Goeldi, Av. Magalhães Barata, 376, Belém, Pará, Brazil
| | - Diego César Batista Mariano
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Frederico Chaves Carvalho
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raquel C de Melo-Minardi
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Robert Tew Boyle
- Graduate Program in Physiological Sciences (PPGCF), Federal University of Rio Grande - FURG, Av. Italy, s/n - km 8 - Carreiros, Rio Grande, Rio Grande do Sul, Brazil
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Safarzadeh Kozani P, Safarzadeh Kozani P, Rahbarizadeh F. Humanization of the antigen-recognition domain does not impinge on the antigen-binding, cytokine secretion, and antitumor reactivity of humanized nanobody-based CD19-redirected CAR-T cells. J Transl Med 2024; 22:679. [PMID: 39054481 PMCID: PMC11271212 DOI: 10.1186/s12967-024-05461-8] [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: 03/22/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND The immunogenicity of the antigen-recognition domains of chimeric antigen receptor (CAR)-T cells leads to immune responses that may compromise the antitumor effects of the adoptively transferred T cells. Herein, we attempt to humanize a CD19-specific VHH (named H85) using in silico techniques and investigate the impact of antigen-recognition domain humanization on CAR expression and density, cytokine secretion, and cytolytic reactivity of CAR-T cells based on the humanized VHH. METHODS H85 was humanized (named HuH85), and then HuH85 was compared with H85 in terms of conformational structure, physicochemical properties, antigenicity and immunogenicity, solubility, flexibility, stability, and CD19-binding capacity using in silico techniques. Next, H85CAR-T cells and HuH85CAR-T cells were developed and CAR expression and surface density were assessed via flow cytometry. Ultimately, the antitumor reactivity and secreted levels of IFN-γ, IL-2, and TNF-α were assessed following the co-cultivation of the CAR-T cells with Ramos, Namalwa, and K562 cells. RESULTS In silico findings demonstrated no negative impacts on HuH85 as a result of humanization. Ultimately, H85CAR and HuH85CAR could be surface-expressed on transduced T cells at comparable levels as assessed via mean fluorescence intensity. Moreover, H85CAR-T cells and HuH85CAR-T cells mediated comparable antitumor effects against Ramos and Namalwa cells and secreted comparable levels of IFN-γ, IL-2, and TNF-α following co-cultivation. CONCLUSION HuH85 can be used to develop immunotherapeutics against CD19-associated hematologic malignancies. Moreover, HuH85CAR-T cells must be further investigated in vitro and in preclinical xenograft models of CD19+ leukemias and lymphomas before advancing into clinical trials.
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Affiliation(s)
- Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran
| | - Pouya Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
- Research and Development Center of Biotechnology, Tarbiat Modares University, Tehran, Iran.
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Oladipo EK, Ojo TO, Elegbeleye OE, Bolaji OQ, Oyewole MP, Ogunlana AT, Olalekan EO, Abiodun B, Adediran DA, Obideyi OA, Olufemi SE, Salamatullah AM, Bourhia M, Younous YA, Adelusi TI. Exploring the nuclear proteins, viral capsid protein, and early antigen protein using immunoinformatic and molecular modeling approaches to design a vaccine candidate against Epstein Barr virus. Sci Rep 2024; 14:16798. [PMID: 39039173 PMCID: PMC11263613 DOI: 10.1038/s41598-024-66828-x] [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: 01/29/2024] [Accepted: 07/04/2024] [Indexed: 07/24/2024] Open
Abstract
The available Epstein Barr virus vaccine has tirelessly harnessed the gp350 glycoprotein as its target epitope, but the result has not been preventive. Right here, we designed a global multi-epitope vaccine for EBV; with special attention to making sure all strains and preventive antigens are covered. Using a robust computational vaccine design approach, our proposed vaccine is armed with 6-16 mers linear B-cell epitopes, 4-9 mer CTL epitopes, and 8-15 mer HTL epitopes which are verified to induce interleukin 4, 10 & IFN-gamma. We employed deep computational mining coupled with expert intelligence in designing the vaccine, using human Beta defensin-3-which has been reported to induce the same TLRs as EBV-as the adjuvant. The tendency of the vaccine to cause autoimmune disorder is quenched by the assurance that the construct contains no EBNA-1 homolog. The protein vaccine construct exhibited excellent physicochemical attributes such as Aliphatic index 59.55 and GRAVY - 0.710; and a ProsaWeb Z score of - 3.04. Further computational analysis revealed the vaccine docked favorably with EBV indicted TLR 1, 2, 4 & 9 with satisfactory interaction patterns. With global coverage of 85.75% and the stable molecular dynamics result obtained for the best two interactions, we are optimistic that our nontoxic, non-allergenic multi-epitope vaccine will help to ameliorate the EBV-associated diseases-which include various malignancies, tumors, and cancers-preventively.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, 232104, Nigeria
| | - Taiwo Ooreoluwa Ojo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Oluwabamise Emmanuel Elegbeleye
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Olawale Quadri Bolaji
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Moyosoluwa Precious Oyewole
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
- Department of Biochemistry, Bowen University, Iwo, 232101, Nigeria
| | - Abdeen Tunde Ogunlana
- Institute of Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Ibadan, 200005, Nigeria
| | - Emmanuel Obanijesu Olalekan
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Bamidele Abiodun
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Daniel Adewole Adediran
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
| | | | - Seun Elijah Olufemi
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
| | - Ahmad Mohammad Salamatullah
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, 11, P.O. Box 2460, 11451, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Therapeutic and Organic Chemistry, Faculty of Pharmacy, University of Montpellier, Montpellier, 34000, France
| | | | - Temitope Isaac Adelusi
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria.
- Department of Surgery, School of Medicine, University of Connecticut Health, Farmington Ave, Farmington, CT, 06030, USA.
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Bárcenas O, Kuriata A, Zalewski M, Iglesias V, Pintado-Grima C, Firlik G, Burdukiewicz M, Kmiecik S, Ventura S. Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation. Nucleic Acids Res 2024; 52:W170-W175. [PMID: 38738618 PMCID: PMC11223845 DOI: 10.1093/nar/gkae382] [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: 03/11/2024] [Revised: 04/11/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Protein aggregation is behind the genesis of incurable diseases and imposes constraints on drug discovery and the industrial production and formulation of proteins. Over the years, we have been advancing the Aggresscan3D (A3D) method, aiming to deepen our comprehension of protein aggregation and assist the engineering of protein solubility. Since its inception, A3D has become one of the most popular structure-based aggregation predictors because of its performance, modular functionalities, RESTful service for extensive screenings, and intuitive user interface. Building on this foundation, we introduce Aggrescan4D (A4D), significantly extending A3D's functionality. A4D is aimed at predicting the pH-dependent aggregation of protein structures, and features an evolutionary-informed automatic mutation protocol to engineer protein solubility without compromising structure and stability. It also integrates precalculated results for the nearly 500,000 jobs in the A3D Model Organisms Database and structure retrieval from the AlphaFold database. Globally, A4D constitutes a comprehensive tool for understanding, predicting, and designing solutions for specific protein aggregation challenges. The A4D web server and extensive documentation are available at https://biocomp.chem.uw.edu.pl/a4d/. This website is free and open to all users without a login requirement.
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Affiliation(s)
- Oriol Bárcenas
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Aleksander Kuriata
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Mateusz Zalewski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, 15-369 Białystok, Poland
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Grzegorz Firlik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, 15-369 Białystok, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Nag S, Stany B, Mishra S, Kumar S, Mohanto S, Ahmed MG, Mathew B, Subramaniyan V. Multireceptor Analysis for Evaluating the Antidiabetic Efficacy of Karanjin: A Computational Approach. Endocrinol Diabetes Metab 2024; 7:e509. [PMID: 38982323 PMCID: PMC11233261 DOI: 10.1002/edm2.509] [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: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/23/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Diabetes mellitus, notably type 2, is a rising global health challenge, prompting the need for effective management strategies. Common medications such as metformin, insulin, repaglinide and sitagliptin can induce side effects like gastrointestinal disturbances, hypoglycemia, weight gain and specific organ risks. Plant-derived therapies like Karanjin from Pongamia pinnata present promising alternatives due to their historical use, holistic health benefits and potentially fewer adverse effects. This study employs in silico analysis to explore Karanjin's interactions with diabetes-associated receptors, aiming to unveil its therapeutic potential while addressing the limitations and side effects associated with conventional medications. METHODOLOGY The research encompassed the selection of proteins from the Protein Data Bank (PDB), followed by structural refinement processes and optimization. Ligands such as Karanjin and standard drugs were retrieved from PubChem, followed by a comprehensive analysis of their ADMET profiling and pharmacokinetic properties. Protein-ligand interactions were evaluated through molecular docking using AutoDockTools 1.5.7, followed by the analysis of structural stability using coarse-grained simulations with CABS Flex 2.0. Molecular dynamics simulations were performed using Desmond 7.2 and the OPLS4 force field to explore how Karanjin interacts with proteins over 100 nanoseconds, focusing on the dynamics and structural stability. RESULTS Karanjin, a phytochemical from Pongamia pinnata, shows superior drug candidate potential compared to common medications, offering advantages in efficacy and reduced side effects. It adheres to drug-likeness criteria and exhibits optimal ADMET properties, including moderate solubility, high gastrointestinal absorption and blood-brain barrier penetration. Molecular docking revealed Karanjin's highest binding energy against receptor 3L2M (Pig pancreatic alpha-amylase) at -9.1 kcal/mol, indicating strong efficacy potential. Molecular dynamics simulations confirmed stable ligand-protein complexes with minor fluctuations in RMSD and RMSF, suggesting robust interactions with receptors 3L2M. CONCLUSION Karanjin demonstrates potential in pharmaceutical expansion for treating metabolic disorders such as diabetes, as supported by computational analysis. Prospects for Karanjin in pharmaceutical development include structural modifications for enhanced efficacy and safety. Nanoencapsulation may improve bioavailability and targeted delivery to pancreatic cells, while combination therapies could optimize treatment outcomes in diabetes management. Clinical trials and experimental studies are crucial to validate its potential as a novel therapeutic agent.
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Affiliation(s)
- Sagnik Nag
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - B Stany
- Department of Biomedical Sciences, School of Bio-Sciences & Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Shatakshi Mishra
- Department of Biomedical Sciences, School of Bio-Sciences & Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, India
| | - Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka, India
| | - Mohammed Gulzar Ahmed
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to Be University), Mangalore, Karnataka, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, India
| | - Vetriselvan Subramaniyan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
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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.
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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
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Erkanli ME, El-Halabi K, Kang TK, Kim JR. Hotspot Wizard-informed engineering of a hyperthermophilic β-glucosidase for enhanced enzyme activity at low temperatures. Biotechnol Bioeng 2024; 121:2079-2090. [PMID: 38682557 DOI: 10.1002/bit.28732] [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: 02/03/2024] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
Hyperthermophilic enzymes serve as an important source of industrial enzymes due to their high thermostability. Unfortunately, most hyperthermophilic enzymes suffer from reduced activity at low temperatures (e.g., ambient temperature), limiting their applicability. In addition, evolving hyperthermophilic enzymes to increase low temperature activity without compromising other desired properties is generally difficult. In the current study, a variant of β-glucosidase from Pyrococcus furiosus (PfBGL) was engineered to enhance enzyme activity at low temperatures through the construction of a saturation mutagenesis library guided by the HotSpot Wizard analysis, followed by its screening for activity and thermostability. From this library construction and screening, one PfBGL mutant, PfBGL-A4 containing Q214S/A264S/F344I mutations, showed an over twofold increase in β-glucosidase activity at 25 and 50°C compared to the wild type, without compromising high-temperature activity, thermostability and substrate specificity. Our experimental and computational characterizations suggest that the findings with PfBGL-A4 may be due to the elevation of local conformational flexibility around the active site, while slightly compacting the global protein structure. This study showcases the potential of HotSpot Wizard-informed engineering of hyperthermophilic enzymes and underscores the interplays among temperature, enzyme activity, and conformational flexibility in these enzymes.
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Affiliation(s)
- Mehmet Emre Erkanli
- Department of Chemical and Biomolecular Engineering, New York University, Brooklyn, New York, USA
| | - Khalid El-Halabi
- Department of Chemical and Biomolecular Engineering, New York University, Brooklyn, New York, USA
| | - Ted Keunsil Kang
- Department of Chemical and Biomolecular Engineering, New York University, Brooklyn, New York, USA
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering, New York University, Brooklyn, New York, USA
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Pumchan A, Proespraiwong P, Sawatdichaikul O, Phurahong T, Hirono I, Unajak S. Computational design of novel chimeric multiepitope vaccine against bacterial and viral disease in tilapia (Oreochromis sp.). Sci Rep 2024; 14:14048. [PMID: 38890454 PMCID: PMC11189486 DOI: 10.1038/s41598-024-64383-z] [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: 02/13/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
Regarding several infectious diseases in fish, multiple vaccinations are not favorable. The chimeric multiepitope vaccine (CMEV) harboring several antigens for multi-disease prevention would enhance vaccine efficiency in terms of multiple disease prevention. Herein, the immunogens of tilapia's seven pathogens including E. tarda, F. columnare, F. noatunensis, S. iniae, S. agalactiae, A. hydrophila, and TiLV were used for CMEV design. After shuffling and annotating the B-cell epitopes, 5,040 CMEV primary protein structures were obtained. Secondary and tertiary protein structures were predicted by AlphaFold2 creating 25,200 CMEV. Proper amino acid alignment in the secondary structures was achieved by the Ramachandran plot. In silico determination of physiochemical and other properties including allergenicity, antigenicity, glycosylation, and conformational B-cell epitopes were determined. The selected CMEV (OSLM0467, OSLM2629, and OSLM4294) showed a predicted molecular weight (MW) of 70 kDa, with feasible sites of N- and O-glycosylation, and a number of potentially conformational B-cell epitope residues. Molecular docking, codon optimization, and in-silico cloning were tested to evaluate the possibility of protein expression. Those CMEVs will further elucidate in vitro and in vivo to evaluate the efficacy and specific immune response. This research will highlight the new era of vaccines designed based on in silico structural vaccine design.
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Affiliation(s)
- Ansaya Pumchan
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
- Kasetsart Vaccines and Bio-Product Innovation Centre, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
| | - Porranee Proespraiwong
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
- Kasetsart Vaccines and Bio-Product Innovation Centre, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
| | - Orathai Sawatdichaikul
- Department of Nutrition and Health, Institute of Food Research and Product Development, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
| | - Thararat Phurahong
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
- Kasetsart Vaccines and Bio-Product Innovation Centre, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand
| | - Ikuo Hirono
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-KU, Tokyo, 108-8477, Japan
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand.
- Kasetsart Vaccines and Bio-Product Innovation Centre, Kasetsart University, 50 Ngam Wong Wan, Chatuchak, 10900, Bangkok, Thailand.
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Shankar SS, Banarjee R, Jathar SM, Rajesh S, Ramasamy S, Kulkarni MJ. De novo structure prediction of meteorin and meteorin-like protein for identification of domains, functional receptor binding regions, and their high-risk missense variants. J Biomol Struct Dyn 2024; 42:4522-4536. [PMID: 37288801 DOI: 10.1080/07391102.2023.2220804] [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: 03/07/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023]
Abstract
Meteorin (Metrn) and Meteorin-like (Metrnl) are homologous secreted proteins involved in neural development and metabolic regulation. In this study, we have performed de novo structure prediction and analysis of both Metrn and Metrnl using Alphafold2 (AF2) and RoseTTAfold (RF). Based on the domain and structural homology analysis of the predicted structures, we have identified that these proteins are composed of two functional domains, a CUB domain and an NTR domain, connected by a hinge/loop region. We have identified the receptor binding regions of Metrn and Metrnl using the machine-learning tools ScanNet and Masif. These were further validated by docking Metrnl with its reported KIT receptor, thus establishing the role of each domain in the receptor interaction. Also, we have studied the effect of non-synonymous SNPs on the structure and function of these proteins using an array of bioinformatics tools and selected 16 missense variants in Metrn and 10 in Metrnl that can affect the protein stability. This is the first study to comprehensively characterize the functional domains of Metrn and Metrnl at their structural level and identify the functional domains, and protein binding regions. This study also highlights the interaction mechanism of the KIT receptor and Metrnl. The predicted deleterious SNPs will allow further understanding of the role of these variants in modulating the plasma levels of these proteins in disease conditions such as diabetes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Shiva Shankar
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Reema Banarjee
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Swaraj M Jathar
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - S Rajesh
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Sureshkumar Ramasamy
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Mahesh J Kulkarni
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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10
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Pedretti M, Fernández-Rodríguez C, Conter C, Oyenarte I, Favretto F, di Matteo A, Dominici P, Petrosino M, Martinez-Chantar ML, Majtan T, Astegno A, Martínez-Cruz LA. Catalytic specificity and crystal structure of cystathionine γ-lyase from Pseudomonas aeruginosa. Sci Rep 2024; 14:9364. [PMID: 38654065 PMCID: PMC11039470 DOI: 10.1038/s41598-024-57625-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
The escalating drug resistance among microorganisms underscores the urgent need for innovative therapeutic strategies and a comprehensive understanding of bacteria's defense mechanisms against oxidative stress and antibiotics. Among the recently discovered barriers, the endogenous production of hydrogen sulfide (H2S) via the reverse transsulfuration pathway, emerges as a noteworthy factor. In this study, we have explored the catalytic capabilities and crystal structure of cystathionine γ-lyase from Pseudomonas aeruginosa (PaCGL), a multidrug-opportunistic pathogen chiefly responsible for nosocomial infections. In addition to a canonical L-cystathionine hydrolysis, PaCGL efficiently catalyzes the production of H2S using L-cysteine and/or L-homocysteine as alternative substrates. Comparative analysis with the human enzyme and counterparts from other pathogens revealed distinct structural features within the primary enzyme cavities. Specifically, a distinctly folded entrance loop could potentially modulate the access of substrates and/or inhibitors to the catalytic site. Our findings offer significant insights into the structural evolution of CGL enzymes across different pathogens and provide novel opportunities for developing specific inhibitors targeting PaCGL.
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Affiliation(s)
- Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Carmen Fernández-Rodríguez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Carolina Conter
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Iker Oyenarte
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Filippo Favretto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Adele di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Maria Petrosino
- Department of Pharmacology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musee 18, Bldg. PER17, 1700, Fribourg, FR, Switzerland
| | - Maria Luz Martinez-Chantar
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Santander, Spain
| | - Tomas Majtan
- Department of Pharmacology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musee 18, Bldg. PER17, 1700, Fribourg, FR, Switzerland
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Luis Alfonso Martínez-Cruz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
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11
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Ben Haj Othmen H, Othman H, Khamessi O, Bettaieb I, Gara S, Kharrat M. Overexpression of WT1 in all molecular subtypes of breast cancer and its impact on survival: exploring oncogenic and tumor suppressor roles of distinct WT1 isoforms. Mol Biol Rep 2024; 51:544. [PMID: 38642153 DOI: 10.1007/s11033-024-09450-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/15/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Breast cancer is a highly heterogeneous solid tumor, posing challenges in developing targeted therapies effective for all mammary carcinoma subtypes. WT1 emerges as a promising target for breast cancer therapy due to its potential oncogenic role in various cancer types. Previous works have yielded inconsistent results. Therefore, further studies are needed to clarify the behavior of this complex gene in breast cancer. METHODS AND RESULTS In this study, we examined WT1 expression in both Formalin Fixed Paraffin Embedded breast tumors (n = 41) and healthy adjacent tissues (n = 41) samples from newly diagnosed cases of ductal invasive breast cancer. The fold change in gene expression between the tumor and healthy tissue was determined by calculating 2-∆∆Ct. Disease-free survival analysis was computed using the Kaplan-Meier method. To identify the expression levels of different WT1 isoforms, we explored the ISOexpresso database. Relative quantification of the WT1 gene revealed an overexpression of WT1 in most cases. The percentage of patients surviving free of disease at 8 years of follow-up was lower in the group overexpressing WT1 compared to the group with down-regulated WT1. CONCLUSIONS Interestingly, this overexpression was observed in all molecular subtypes of invasive breast cancer, underscoring the significance of WT1 as a potential target in all these subtypes. The observed WT1 down-expression in a few cases of invasive breast cancer, associated with better survival outcomes, may correspond to the down-regulation of a particular WT1-KTS (-) isoform: the WT1 A isoform (EX5-/KTS-). The co-expression of this WT1 oncogenic isoform with a regulated WT1- tumor suppressor isoform, such as the major WT1 F isoform (EX5-/KTS +), could also explain such survival outcomes. Due to its capacity to adopt dual roles, it becomes imperative to conduct individual molecular expression profiling of the WT1 gene. Such an approach holds great promise in the development of personalized treatment strategies for breast cancer.
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Affiliation(s)
- Hind Ben Haj Othmen
- Human Genetics Laboratory LR99ES10, Faculty of Medicine of Tunis, University of Tunis El Manar, 1007, Tunis, Tunisia.
| | - Houcemeddine Othman
- Laboratory of Cytogenetics, Molecular Genetics and Biology of Human Reproduction, University Hospital Farhat Hached, Sousse, Tunisia
| | - Oussema Khamessi
- Biotechnology Institut of Sidi Thabet, University of Manouba, Ariana BP-66, 2010, Manouba, Tunisia
| | - Ilhem Bettaieb
- Laboratory of Immunohistocytology, Salah Azaiez Cancer Institute, 1006, Tunis, Tunisia
| | - Sonia Gara
- Human Genetics Laboratory LR99ES10, Faculty of Medicine of Tunis, University of Tunis El Manar, 1007, Tunis, Tunisia
- Laboratory of Clinical Biochemistry, Salah Azaiez Cancer Institute, 1006, Tunis, Tunisia
| | - Maher Kharrat
- Human Genetics Laboratory LR99ES10, Faculty of Medicine of Tunis, University of Tunis El Manar, 1007, Tunis, Tunisia
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12
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Tripp A, Braun M, Wieser F, Oberdorfer G, Lechner H. Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering. Chembiochem 2024:e202400092. [PMID: 38634409 DOI: 10.1002/cbic.202400092] [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: 01/31/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Enzyme engineering, though pivotal across various biotechnological domains, is often plagued by its time-consuming and labor-intensive nature. This review aims to offer an overview of supportive in silico methodologies for this demanding endeavor. Starting from methods to predict protein structures, to classification of their activity and even the discovery of new enzymes we continue with describing tools used to increase thermostability and production yields of selected targets. Subsequently, we discuss computational methods to modulate both, the activity as well as selectivity of enzymes. Last, we present recent approaches based on cutting-edge machine learning methods to redesign enzymes. With exception of the last chapter, there is a strong focus on methods easily accessible via web-interfaces or simple Python-scripts, therefore readily useable for a diverse and broad community.
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Affiliation(s)
- Adrian Tripp
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Markus Braun
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Florian Wieser
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Gustav Oberdorfer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
| | - Horst Lechner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
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13
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Ahmad I, Singh AK, Mohd S, Katari SK, Nalamolu RM, Ahmad A, Baothman OA, Hosawi SA, Altayeb H, Nadeem MS, Ahmad V. In Silico Insights into the Arsenic Binding Mechanism Deploying Application of Computational Biology-Based Toolsets. ACS OMEGA 2024; 9:7529-7544. [PMID: 38405466 PMCID: PMC10882604 DOI: 10.1021/acsomega.3c06313] [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: 08/24/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
An assortment of environmental matrices includes arsenic (As) in its different oxidation states, which is often linked to concerns that pose a threat to public health worldwide. The current difficulty lies in addressing toxicological concerns and achieving sustained detoxification of As. Multiple conventional degradation methods are accessible; however, they are indeed labor-intensive, expensive, and reliant on prolonged laboratory evaluations. Molecular interaction and atomic level degradation mechanisms for enzyme-As exploration are, however, underexplored in those approaches. A feasible approach in this case for tackling this accompanying concern of As might be to cope with undertaking multivalent computational methodologies and tools. This work aimed to provide molecular-level insight into the enzyme-aided As degradation mechanism. AutoDock Vina, CABS-flex 2.0, and Desmond high-performance molecular dynamics simulation (MDS) were utilized in the current investigation to simulate multivalent molecular processes on two protein sets: arsenate reductase (ArsC) and laccase (LAC) corresponding arsenate (ART) and arsenite (AST), which served as model ligands to comprehend binding, conformational, and energy attributes. The structural configurations of both proteins exhibited variability in flexibility and structure framework within the range of 3.5-4.5 Å. The LAC-ART complex exhibited the lowest calculated binding affinity, measuring -5.82 ± 0.01 kcal/mol. Meanwhile, active site residues ILE-200 and HIS-206 were demonstrated to engage in H-bonding with the ART ligand. In contrast to ArsC, the ligand binding affinity of this bound complex was considerably greater. Additional validation of docked complexes was carried out by deploying Desmond MDS of 100 ns to capture protein and ligand conformation behavior. The system achieved stability during the 100 ns simulation run, as confirmed by the average P-L RMSD, which was ∼1 Å. As a preliminary test of the enzyme's ability to catalyze As species, corresponding computational insights might be advantageous for bridging gaps and regulatory consideration.
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Affiliation(s)
- Imran Ahmad
- Department
of Biochemistry, King George’s Medical
University, Lucknow, Uttar Pradesh 226003, India
- Environmental
Toxicology Group, CSIR-Indian Institute
of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anil Kumar Singh
- Environmental
Toxicology Group, CSIR-Indian Institute
of Toxicology Research (CSIR-IITR), Vishvigyan Bhavan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shayan Mohd
- Department
of Bioengineering, Faculty of Engineering, Integral University, Dasauli, Kursi Road, Lucknow 226026, India
| | - Sudheer Kumar Katari
- Department
of Biotechnology, Vignan’s Foundation
for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Ravina Madhulitha Nalamolu
- Department
of Biotechnology, Vignan’s Foundation
for Science, Technology & Research, Vadlamudi, Andhra Pradesh 522213, India
| | - Abrar Ahmad
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Othman A. Baothman
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Salman A. Hosawi
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Hisham Altayeb
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Kingdom
of Saudi Arabia
| | - Varish Ahmad
- Department
of Health Information Technology, Faculty of Applied Studies, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
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14
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Timilsina U, Ivey EB, Duffy S, Plianchaisuk A, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito J, Sato K, Stavrou S. SARS-CoV-2 ORF7a Mutation Found in BF.5 and BF.7 Sublineages Impacts Its Functions. Int J Mol Sci 2024; 25:2351. [PMID: 38397027 PMCID: PMC10889720 DOI: 10.3390/ijms25042351] [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: 01/25/2024] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
A feature of the SARS-CoV-2 Omicron subvariants BF.5 and BF.7 that recently circulated mainly in China and Japan was the high prevalence of the ORF7a: H47Y mutation, in which the 47th residue of ORF7a has been mutated from a histidine (H) to a tyrosine (Y). Here, we evaluated the effect of this mutation on the three main functions ascribed to the SARS-CoV-2 ORF7a protein. Our findings show that H47Y mutation impairs the ability of SARS-CoV-2 ORF7a to antagonize the type I interferon (IFN-I) response and to downregulate major histocompatibility complex I (MHC-I) cell surface levels, but had no effect in its anti-SERINC5 function. Overall, our results suggest that the H47Y mutation of ORF7a affects important functions of this protein, resulting in changes in virus pathogenesis.
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Affiliation(s)
- Uddhav Timilsina
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA; (U.T.); (E.B.I.); (S.D.)
| | - Emily B. Ivey
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA; (U.T.); (E.B.I.); (S.D.)
| | - Sean Duffy
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA; (U.T.); (E.B.I.); (S.D.)
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8369, Japan; (A.P.); (J.I.); (K.S.)
| | | | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8369, Japan; (A.P.); (J.I.); (K.S.)
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8369, Japan; (A.P.); (J.I.); (K.S.)
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8369, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8581, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0862, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Spyridon Stavrou
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA; (U.T.); (E.B.I.); (S.D.)
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15
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Doni D, Cavallari E, Noguera ME, Gentili HG, Cavion F, Parisi G, Fornasari MS, Sartori G, Santos J, Bellanda M, Carbonera D, Costantini P, Bortolus M. Searching for Frataxin Function: Exploring the Analogy with Nqo15, the Frataxin-like Protein of Respiratory Complex I from Thermus thermophilus. Int J Mol Sci 2024; 25:1912. [PMID: 38339189 PMCID: PMC10855754 DOI: 10.3390/ijms25031912] [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: 12/23/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Nqo15 is a subunit of respiratory complex I of the bacterium Thermus thermophilus, with strong structural similarity to human frataxin (FXN), a protein involved in the mitochondrial disease Friedreich's ataxia (FRDA). Recently, we showed that the expression of recombinant Nqo15 can ameliorate the respiratory phenotype of FRDA patients' cells, and this prompted us to further characterize both the Nqo15 solution's behavior and its potential functional overlap with FXN, using a combination of in silico and in vitro techniques. We studied the analogy of Nqo15 and FXN by performing extensive database searches based on sequence and structure. Nqo15's folding and flexibility were investigated by combining nuclear magnetic resonance (NMR), circular dichroism, and coarse-grained molecular dynamics simulations. Nqo15's iron-binding properties were studied using NMR, fluorescence, and specific assays and its desulfurase activation by biochemical assays. We found that the recombinant Nqo15 isolated from complex I is monomeric, stable, folded in solution, and highly dynamic. Nqo15 does not share the iron-binding properties of FXN or its desulfurase activation function.
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Affiliation(s)
- Davide Doni
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Eva Cavallari
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
- Grenoble Alpes University, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Martin Ezequiel Noguera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
- Institute of Biological Chemistry and Physical Chemistry, Dr Alejandro Paladini (UBA-CONICET), University of Buenos Aires, Junín 956, Buenos Aires 1113AAD, Argentina
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Hernan Gustavo Gentili
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
| | - Federica Cavion
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Gustavo Parisi
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Maria Silvina Fornasari
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy;
| | - Javier Santos
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
| | - Massimo Bellanda
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
- Consiglio Nazionale delle Ricerche Institute of Biomolecular Chemistry, 35131 Padova, Italy
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
| | - Paola Costantini
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
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16
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Sankhala RS, Dussupt V, Chen WH, Bai H, Martinez EJ, Jensen JL, Rees PA, Hajduczki A, Chang WC, Choe M, Yan L, Sterling SL, Swafford I, Kuklis C, Soman S, King J, Corbitt C, Zemil M, Peterson CE, Mendez-Rivera L, Townsley SM, Donofrio GC, Lal KG, Tran U, Green EC, Smith C, de Val N, Laing ED, Broder CC, Currier JR, Gromowski GD, Wieczorek L, Rolland M, Paquin-Proulx D, van Dyk D, Britton Z, Rajan S, Loo YM, McTamney PM, Esser MT, Polonis VR, Michael NL, Krebs SJ, Modjarrad K, Joyce MG. Antibody targeting of conserved sites of vulnerability on the SARS-CoV-2 spike receptor-binding domain. Structure 2024; 32:131-147.e7. [PMID: 38157856 PMCID: PMC11145656 DOI: 10.1016/j.str.2023.11.015] [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: 05/05/2023] [Revised: 09/14/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
Given the continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs), immunotherapeutics that target conserved epitopes on the spike (S) glycoprotein have therapeutic advantages. Here, we report the crystal structure of the SARS-CoV-2 S receptor-binding domain (RBD) at 1.95 Å and describe flexibility and distinct conformations of the angiotensin-converting enzyme 2 (ACE2)-binding site. We identify a set of SARS-CoV-2-reactive monoclonal antibodies (mAbs) with broad RBD cross-reactivity including SARS-CoV-2 Omicron subvariants, SARS-CoV-1, and other sarbecoviruses and determine the crystal structures of mAb-RBD complexes with Ab246 and CR3022 mAbs targeting the class IV site, WRAIR-2134, which binds the recently designated class V epitope, and WRAIR-2123, the class I ACE2-binding site. The broad reactivity of class IV and V mAbs to conserved regions of SARS-CoV-2 VoCs and other sarbecovirus provides a framework for long-term immunotherapeutic development strategies.
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Affiliation(s)
- Rajeshwer S Sankhala
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Vincent Dussupt
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hongjun Bai
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth J Martinez
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jaime L Jensen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Phyllis A Rees
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes Hajduczki
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - William C Chang
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Misook Choe
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Lianying Yan
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Spencer L Sterling
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Isabella Swafford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caitlin Kuklis
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sandrine Soman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jocelyn King
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Courtney Corbitt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caroline E Peterson
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Letzibeth Mendez-Rivera
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Samantha M Townsley
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gina C Donofrio
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kerri G Lal
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ursula Tran
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ethan C Green
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Clayton Smith
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, MD, USA
| | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Gregory D Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Morgane Rolland
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dominic Paquin-Proulx
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dewald van Dyk
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Zachary Britton
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Saravanan Rajan
- Antibody Discovery and Protein Engineering (ADPE), BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Yueh Ming Loo
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Patrick M McTamney
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mark T Esser
- Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Shelly J Krebs
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - M Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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17
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Badaczewska-Dawid A, Wróblewski K, Kurcinski M, Kmiecik S. Structure prediction of linear and cyclic peptides using CABS-flex. Brief Bioinform 2024; 25:bbae003. [PMID: 38305457 PMCID: PMC10836054 DOI: 10.1093/bib/bbae003] [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: 06/30/2023] [Revised: 12/08/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024] Open
Abstract
The structural modeling of peptides can be a useful aid in the discovery of new drugs and a deeper understanding of the molecular mechanisms of life. Here we present a novel multiscale protocol for the structure prediction of linear and cyclic peptides. The protocol combines two main stages: coarse-grained simulations using the CABS-flex standalone package and an all-atom reconstruction-optimization process using the Modeller program. We evaluated the protocol on a set of linear peptides and two sets of cyclic peptides, with cyclization through the backbone and disulfide bonds. A comparison with other state-of-the-art tools (APPTEST, PEP-FOLD, ESMFold and AlphaFold implementation in ColabFold) shows that for most cases, AlphaFold offers the highest resolution. However, CABS-flex is competitive, particularly when it comes to short linear peptides. As demonstrated, the protocol performance can be further improved by combination with the residue-residue contact prediction method or more efficient scoring. The protocol is included in the CABS-flex standalone package along with online documentation to aid users in predicting the structure of peptides and mini-proteins.
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Affiliation(s)
| | - Karol Wróblewski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Mateusz Kurcinski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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18
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Badaczewska-Dawid AE, Kuriata A, Pintado-Grima C, Garcia-Pardo J, Burdukiewicz M, Iglesias V, Kmiecik S, Ventura S. A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms. Nucleic Acids Res 2024; 52:D360-D367. [PMID: 37897355 PMCID: PMC10767922 DOI: 10.1093/nar/gkad942] [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: 08/14/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Protein aggregation has been associated with aging and different pathologies and represents a bottleneck in the industrial production of biotherapeutics. Numerous past studies performed in Escherichia coli and other model organisms have allowed to dissect the biophysical principles underlying this process. This knowledge fuelled the development of computational tools, such as Aggrescan 3D (A3D) to forecast and re-design protein aggregation. Here, we present the A3D Model Organism Database (A3D-MODB) http://biocomp.chem.uw.edu.pl/A3D2/MODB, a comprehensive resource for the study of structural protein aggregation in the proteomes of 12 key model species spanning distant biological clades. In addition to A3D predictions, this resource incorporates information useful for contextualizing protein aggregation, including membrane protein topology and structural model confidence, as an indirect reporter of protein disorder. The database is openly accessible without any need for registration. We foresee A3D-MOBD evolving into a central hub for conducting comprehensive, multi-species analyses of protein aggregation, fostering the development of protein-based solutions for medical, biotechnological, agricultural and industrial applications.
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Affiliation(s)
| | - Aleksander Kuriata
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, 15-369, Białystok, Poland
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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19
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Mahnoor I, Shabbir H, Nawaz S, Aziz K, Aziz U, Khalid K, Irum S, Andleeb S. Characterization of exclusively non-commensal Neisseria gonorrhoeae pangenome to prioritize globally conserved and thermodynamically stable vaccine candidates using immune-molecular dynamic simulations. Microb Pathog 2023; 185:106439. [PMID: 37944674 DOI: 10.1016/j.micpath.2023.106439] [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: 07/28/2023] [Revised: 10/19/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Neisseria gonorrhoeae (Ngo) has emerged as a global threat leading to one of the most common sexually transmitted diseases in the world. It has also become one of the leading antimicrobial resistant organisms, resulting in fewer treatment options and an increased morbidity. Therefore, in recent years, there has been an increased focus on the development of new treatments and preventive strategies to combat its infection. In this study, we have combined the most conserved epitopes from the completely assembled strains of Ngo to develop a universal and a thermodynamically stable vaccine candidate. For our vaccine design, the epitopes were selected for their high immunogenicity, non-allergenicity and non-cytotoxicity, making them the ideal candidates for vaccine development. For the screening process, several reverse vaccinology tools were employed to rigorously extract non-homologous and immunogenic epitopes from the selected proteins. Consequently, a total number of 3 B-cell epitopes and 6 T-cell epitopes were selected and joined by multiple immune-modulating adjuvants and linkers to generate a promiscuous immune response. Additionally, the stability and flexible nature of the vaccine construct was confirmed using various molecular dynamic simulation tools. Overall, the vaccine candidate showed promising binding affinity to various HLA alleles and TLR receptors; however, further studies are needed to assess its efficacy in-vivo. In this way, we have designed a multi-subunit vaccine candidate to potentially combat and control the spread of N. gonorrhoeae.
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Affiliation(s)
- Iqra Mahnoor
- Atta-ur-Rehman School of Biosciences, National University of Science and Technology, Islamabad, Pakistan.
| | - Hamna Shabbir
- Atta-ur-Rehman School of Biosciences, National University of Science and Technology, Islamabad, Pakistan.
| | - Shabana Nawaz
- Atta-ur-Rehman School of Biosciences, National University of Science and Technology, Islamabad, Pakistan.
| | - Kinza Aziz
- Atta-ur-Rehman School of Biosciences, National University of Science and Technology, Islamabad, Pakistan.
| | - Ubair Aziz
- School of Interdisciplinary Engineering & Sciences National University of Science and Technology, Islamabad, Pakistan.
| | - Kashaf Khalid
- Atta-ur-Rehman School of Biosciences, National University of Science and Technology, Islamabad, Pakistan.
| | - Sidra Irum
- Atta-ur-Rehman School of Biosciences, National University of Science and Technology, Islamabad, Pakistan.
| | - Saadia Andleeb
- Atta-ur-Rehman School of Biosciences, National University of Science and Technology, Islamabad, Pakistan.
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20
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Morshed AKMH, Al Azad S, Mia MAR, Uddin MF, Ema TI, Yeasin RB, Srishti SA, Sarker P, Aurthi RY, Jamil F, Samia NSN, Biswas P, Sharmeen IA, Ahmed R, Siddiquy M, Nurunnahar. Oncoinformatic screening of the gene clusters involved in the HER2-positive breast cancer formation along with the in silico pharmacodynamic profiling of selective long-chain omega-3 fatty acids as the metastatic antagonists. Mol Divers 2023; 27:2651-2672. [PMID: 36445532 DOI: 10.1007/s11030-022-10573-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022]
Abstract
The HER2-positive patients occupy ~ 30% of the total breast cancer patients globally where no prevalent drugs are available to mitigate the frequent metastasis clinically except lapatinib and neratinib. This scarcity reinforced researchers' quest for new medications where natural substances are significantly considered. Valuing the aforementioned issues, this research aimed to study the ERBB2-mediated string networks that work behind the HER2-positive breast cancer formation regarding co-expression, gene regulation, GAMA-receptor-signaling pathway, cellular polarization, and signal inhibition. Following the overexpression, promotor methylation, and survivability profiles of ERBB2, the super docking position of HER2 was identified using the quantum tunneling algorithm. Supramolecular docking was conducted to study the target specificity of EPA and DHA fatty acids followed by a comprehensive molecular dynamic simulation (100 ns) to reveal the RMSD, RMSF, Rg, SASA, H-bonds, and MM/GBSA values. Finally, potential drug targets for EPA and DHA in breast cancer were constructed to determine the drug-protein interactions (DPI) at metabolic stages. Considering the values resulting from the combinational models of the oncoinformatic, pharmacodynamic, and metabolic parameters, long-chain omega-3 fatty acids like EPA and DHA can be considered as potential-targeted therapeutics for HER2-positive breast cancer treatment.
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Affiliation(s)
- A K M Helal Morshed
- Pathology and Pathophysiology Major, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001, Henan Province, People's Republic of China
| | - Salauddin Al Azad
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu Province, People's Republic of China.
| | - Md Abdur Rashid Mia
- Department of Pharmaceutical Technology, Faculty of Pharmacy, International Islamic University Malaysia, 25200, Pahang, Kuantan, Malaysia
| | - Mohammad Fahim Uddin
- College of Material Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, People's Republic of China
| | - Tanzila Ismail Ema
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Rukaiya Binte Yeasin
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | | | - Pallab Sarker
- Department of Medicine, Sher-E-Bangla Medical College Hospital, South Alekanda, Barisal, 8200, Bangladesh
| | - Rubaita Younus Aurthi
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Palashi, Dhaka, 1205, Bangladesh
| | - Farhan Jamil
- Department of Pharmacy, University of Asia Pacific, Farmgate, Dhaka, 1205, Bangladesh
| | | | - Partha Biswas
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Iffat Ara Sharmeen
- School of Data Sciences, Department of Mathematics & Natural Sciences, BRAC University, 66 Mohakhali, Dhaka, 1212, Bangladesh
| | - Rasel Ahmed
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, TS1 3BX, Tees Valley, UK
| | - Mahbuba Siddiquy
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, People's Republic of China
| | - Nurunnahar
- Department of Mathematics, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh
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21
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Panda M, Kalita E, Singh S, Kumar K, Prajapati VK. Nanobody-peptide-conjugate (NPC) for passive immunotherapy against SARS-CoV-2 variants of concern (VoC): a prospective pan-coronavirus therapeutics. Mol Divers 2023; 27:2577-2603. [PMID: 36400898 PMCID: PMC9676808 DOI: 10.1007/s11030-022-10570-x] [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: 10/06/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
The COVID-19 crisis, incited by the zoonotic SARS-CoV-2 virus, has quickly escalated into a catastrophic public health issue and a grave threat to humankind owing to the advent of mutant viruses. Multiple pharmaceutical therapies or biologics envision stopping the virus from spreading further; however, WHO has voiced concerns about the variants of concern (VoCs) inability to respond. Nanobodies are a new class of antibody mimics with binding affinity and specificity similar to classical mAbs, as well as the privileges of a small molecular weight, ease of entry into solid tissues, and binding cryptic epitopes of the antigen. Herein, we investigated multiple putative anti-SARS-CoV-2 nanobodies targeting the Receptor binding domain of the WHO-listed SARS-CoV-2 variants of concern using a comprehensive computational immunoinformatics methodology. With affinity maturation via alanine scanning mutagenesis, we remodeled an ultrapotent nanobody with substantial breadth and potency, exhibiting pico-molar binding affinities against all the VoCs. An antiviral peptide with specificity for ACE-2 receptors was affixed to make it multispecific and discourage viral entry. Collectively, we constructed a broad-spectrum therapeutic biparatopic nanobody-peptide conjugate (NPC) extending coverage to SARS-CoV-2 VoCs RBDs. We PEGylated the biparatopic construct with 20kD maleimide-terminated PEG (MAL-(PEG)n-OMe) to improve its clinical efficacy limiting rapid renal clearance, and performed in silico cloning to facilitate future experimental studies. Our findings suggest that combining biparatopic nanobody conjugate with standard treatment may be a promising bivariate tool for combating viral entry during COVID-19 illness.
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Affiliation(s)
- Mamta Panda
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Elora Kalita
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Ketan Kumar
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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22
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Ameji PJ, Uzairu A, Shallangwa GA, Uba S. Molecular docking-based virtual screening, drug-likeness, and pharmacokinetic profiling of some anti- Salmonella typhimurium cephalosporin derivatives. J Taibah Univ Med Sci 2023; 18:1417-1431. [PMID: 38162870 PMCID: PMC10757315 DOI: 10.1016/j.jtumed.2023.05.021] [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: 12/03/2022] [Revised: 04/25/2023] [Accepted: 05/31/2023] [Indexed: 01/03/2024] Open
Abstract
Objective The rising cases of resistance to existing antibiotic therapies in Salmonella typhimurium has made it necessary to search for novel drug candidates. The present study employed the molecular docking technique to screen a set of antibacterial cephalosporin analogues against penicillin-binding protein 1a (PBP1a) of the bacterium. This is the first study to screen cephalosporin analogues against PBP1a, a protein central to peptidoglycan synthesis in S. typhimurium. Methods Some cephalosporin analogues were retrieved from a drug repository. The structures of the molecules were optimized using the semi-empirical method of Spartan 14 software and were subsequently docked against the active sites of PBP1a using AutoDock vina software. The most potent ligands were chosen as the most promising leads and subsequently subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling using the SwissADME online server and DataWarrior chemoinformatics program. The CABSflex 2.0 server was used to carry out molecular dynamics (MD) simulation on the most stable ligand-protein complex. Results Compounds 3, 23, and 28 with binding affinity (ΔG) values of -9.2, -8.7, and -8.9 kcal/mol, respectively, were selected as the most promising leads. The ligands bound to the active sites of PBP1a via hydrophobic bonds, hydrogen bonds, and electrostatic interactions. Furthermore, ADMET analyses of the ligands revealed that they exhibited sound pharmacokinetic and toxicity profiles. In addition, an MD study revealed that the most active ligand bound favorably and dynamically to the target protein. Conclusion The findings of this research could provide an excellent platform for the discovery and rational design of novel antibiotics against S. typhimurium. Additional in vitro and in vivo studies should be carried out on the drug candidates to validate the findings of this study.
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Affiliation(s)
- Philip John Ameji
- Department of Chemistry, Federal University Lokoja, Lokoja, Kogi State, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | | | - Sani Uba
- Department of Chemistry, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
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23
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Oladipo EK, Ojo TO, Olufemi SE, Irewolede BA, Adediran DA, Abiala AG, Hezekiah OS, Idowu AF, Oladeji YG, Ikuomola MO, Olayinka AT, Akanbi GO, Idowu UA, Olubodun OA, Odunlami FD, Ogunniran JA, Akinro OP, Adegoke HM, Folakanmi EO, Usman TA, Oladokun EF, Oluwasanya GJ, Awobiyi HO, Oluwasegun JA, Akintibubo SA, Jimah EM. Proteome based analysis of circulating SARS-CoV-2 variants: approach to a universal vaccine candidate. Genes Genomics 2023; 45:1489-1508. [PMID: 37548884 DOI: 10.1007/s13258-023-01426-1] [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: 07/16/2022] [Accepted: 07/09/2023] [Indexed: 08/08/2023]
Abstract
The discovery of the first infectious variant in Wuhan, China, in December 2019, has posed concerns over global health due to the spread of COVID-19 and subsequent variants. While the majority of patients experience flu-like symptoms such as cold and fever, a small percentage, particularly those with compromised immune systems, progress from mild illness to fatality. COVID-19 is caused by a RNA virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our approach involved utilizing immunoinformatic to identify vaccine candidates with multiple epitopes and ligand-binding regions in reported SARS-CoV-2 variants. Through analysis of the spike glycoprotein, we identified dominant epitopes for T-cells and B-cells, resulting in a vaccine construct containing two helper T-cell epitopes, six cytotoxic T-cell epitopes, and four linear B-cell epitopes. Prior to conjugation with adjuvants and linkers, all epitopes were evaluated for antigenicity, toxicity, and allergenicity. Additionally, we assessed the vaccine Toll-Like Receptors complex (2, 3, and 4). The vaccine construct demonstrated antigenicity, non-toxicity, and non-allergenicity, thereby enabling the host to generate antibodies with favorable physicochemical characteristics. Furthermore, the 3D structure of the B-cell construct exhibited a ProSA-web z-score plot with a value of -1.71, indicating the reliability of the designed structure. The Ramachandran plot analysis revealed that 99.6% of the amino acid residues in the vaccine subunit were located in the high favored observation region, further establishing its strong candidacy as a vaccination option.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Informatics, Adeleke University, Ede, Osun State, Nigeria.
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria.
| | - Taiwo Ooreoluwa Ojo
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Seun Elijah Olufemi
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Daniel Adewole Adediran
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Asegunloluwa Grace Abiala
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwaseun Samuel Hezekiah
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Akindele Felix Idowu
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Yinmi Gabriel Oladeji
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Microbiology, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Mary Omotoyinbo Ikuomola
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Adenike Titilayo Olayinka
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Gideon Oluwamayowa Akanbi
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Usman Abiodun Idowu
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Odunola Abimbola Olubodun
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Folusho Daniel Odunlami
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - James Akinwumi Ogunniran
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Omodamola Paulina Akinro
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Hadijat Motunrayo Adegoke
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Elizabeth Oluwatoyin Folakanmi
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Elizabeth Folakemi Oladokun
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | | | - Jerry Ayobami Oluwasegun
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Samuel Adebowale Akintibubo
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
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Caron-Godon CA, Della Vecchia S, Romano A, Doccini S, Dal Canto F, Pasquariello R, Rubegni A, Battini R, Santorelli FM, Glerum DM, Nesti C. Novel COX11 Mutations Associated with Mitochondrial Disorder: Functional Characterization in Patient Fibroblasts and Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:16636. [PMID: 38068960 PMCID: PMC10706101 DOI: 10.3390/ijms242316636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Genetic defects in the nuclear encoded subunits and assembly factors of cytochrome c oxidase (mitochondrial complex IV) are very rare and are associated with a wide variety of phenotypes. Biallelic pathogenic variants in the COX11 protein were previously identified in two unrelated children with infantile-onset mitochondrial encephalopathies. Through comprehensive clinical, genetic and functional analyses, here we report on a new patient harboring novel heterozygous variants in COX11, presenting with Leigh-like features, and provide additional experimental evidence for a direct correlation between COX11 protein expression and sensitivity to oxidative stress. To sort out the contribution of the single mutations to the phenotype, we employed a multi-faceted approach using Saccharomyces cerevisiae as a genetically manipulable system, and in silico structure-based analysis of human COX11. Our results reveal differential effects of the two novel COX11 mutations on yeast growth, respiration, and cellular redox status, as well as their potential impact on human protein stability and function. Strikingly, the functional deficits observed in patient fibroblasts are recapitulated in yeast models, validating the conservation of COX11's role in mitochondrial integrity across evolutionarily distant organisms. This study not only expands the mutational landscape of COX11-associated mitochondrial disorders but also underscores the continued translational relevance of yeast models in dissecting complex molecular pathways.
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Affiliation(s)
| | - Stefania Della Vecchia
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Viale Pieraccini, 6, 50139 Florence, Italy;
- Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (S.D.); (F.D.C.); (A.R.); (F.M.S.); (C.N.)
| | - Alessandro Romano
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS Ospedale San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Stefano Doccini
- Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (S.D.); (F.D.C.); (A.R.); (F.M.S.); (C.N.)
| | - Flavio Dal Canto
- Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (S.D.); (F.D.C.); (A.R.); (F.M.S.); (C.N.)
| | | | - Anna Rubegni
- Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (S.D.); (F.D.C.); (A.R.); (F.M.S.); (C.N.)
| | - Roberta Battini
- Developmental Neurology and Neurorehabilitation Unit, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Filippo Maria Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (S.D.); (F.D.C.); (A.R.); (F.M.S.); (C.N.)
| | - D. Moira Glerum
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Claudia Nesti
- Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, IRCCS Stella Maris Foundation, 56128 Pisa, Italy; (S.D.); (F.D.C.); (A.R.); (F.M.S.); (C.N.)
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Acharya R, Shetty SS, Pavan G, Monteiro F, Munikumar M, Naresh S, Kumari NS. AI-Based Homology Modelling of Fatty Acid Transport Protein 1 Using AlphaFold: Structural Elucidation and Molecular Dynamics Exploration. Biomolecules 2023; 13:1670. [PMID: 38002353 PMCID: PMC10669040 DOI: 10.3390/biom13111670] [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: 09/23/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/26/2023] Open
Abstract
Fatty acid transport protein 1 (FATP1) is an integral transmembrane protein that is involved in facilitating the translocation of long-chain fatty acids (LCFA) across the plasma membrane, thereby orchestrating the importation of LCFA into the cell. FATP1 also functions as an acyl-CoA ligase, catalyzing the ATP-dependent formation of fatty acyl-CoA using LCFA and VLCFA (very-long-chain fatty acids) as substrates. It is expressed in various types of tissues and is involved in the regulation of crucial signalling pathways, thus playing a vital role in numerous physiological and pathological conditions. Structural insight about FATP1 is, thus, extremely important for understanding the mechanism of action of this protein and developing efficient treatments against its anomalous expression and dysregulation, which are often associated with pathological conditions such as breast cancer. As of now, there has been no prior prediction or evaluation of the 3D configuration of the human FATP1 protein, hindering a comprehensive understanding of the distinct functional roles of its individual domains. In our pursuit to unravel the structure of the most commonly expressed isoforms of FATP1, we employed the cutting-edge ALPHAFOLD 2 model for an initial prediction of the entire protein's structure. This prediction was complemented by molecular dynamics simulations, focusing on the most promising model. We predicted the structure of FATP1 in silico and thoroughly refined and validated it using coarse and molecular dynamics in the absence of the complete crystal structure. Their relative dynamics revealed the different properties of the characteristic FATP1.
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Affiliation(s)
- Ranjitha Acharya
- Department of Biochemistry, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (R.A.); (F.M.); (S.N.)
| | - Shilpa S. Shetty
- Central Research Laboratory, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (S.S.S.); (G.P.)
| | - Gollapalli Pavan
- Central Research Laboratory, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (S.S.S.); (G.P.)
| | - Flama Monteiro
- Department of Biochemistry, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (R.A.); (F.M.); (S.N.)
| | - Manne Munikumar
- Clinical Division, ICMR-National Institute of Nutrition, Jamai-Osmania (Post), Hyderabad 500007, India;
| | - Sriram Naresh
- Department of Biochemistry, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (R.A.); (F.M.); (S.N.)
| | - Nalilu Suchetha Kumari
- Department of Biochemistry, KS Hegde Medical Academy, Nitte (Deemed to be University), Mangalore 575018, India; (R.A.); (F.M.); (S.N.)
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Martínez-Rodríguez S, Cámara-Artigas A, Gavira JA. First 3-D structural evidence of a native-like intertwined dimer in the acylphosphatase family. Biochem Biophys Res Commun 2023; 682:85-90. [PMID: 37804591 DOI: 10.1016/j.bbrc.2023.09.053] [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: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023]
Abstract
Acylphosphatase (AcP, EC 3.6.1.7) is a small model protein conformed by a ferredoxin-like fold, profoundly studied to get insights into protein folding and aggregation processes. Numerous studies focused on the aggregation and/or amyloidogenic properties of AcPs suggest the importance of edge-β-strands in the process. In this work, we present the first crystallographic structure of Escherichia coli AcP (EcoAcP), showing notable differences with the only available NMR structure for this enzyme. EcoAcP is crystalised as an intertwined dimer formed by replacing a single C-terminal β-strand between two protomers, suggesting a flexible character of the C-terminal edge of EcoAcP. Despite numerous works where AcP from different sources have been used as a model system for protein aggregation, our domain-swapped EcoAcP structure is the first 3-D structural evidence of native-like aggregated species for any AcP reported to date, providing clues on molecular determinants unleashing aggregation.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Avenida de La Investigación 11, Granada, 18071, Spain; Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain.
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Centro de Investigación en Agrosistemas Intensivos Mediterráneos y Biotecnología Agroalimentaria (CIAMBITAL), Carretera de Sacramento S/n, Almería, 04120, Spain
| | - Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain
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Kang S, Kim M, Sun J, Lee M, Min K. Prediction of Protein Aggregation Propensity via Data-Driven Approaches. ACS Biomater Sci Eng 2023; 9:6451-6463. [PMID: 37844262 DOI: 10.1021/acsbiomaterials.3c01001] [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: 10/18/2023]
Abstract
Protein aggregation occurs when misfolded or unfolded proteins physically bind together and can promote the development of various amyloid diseases. This study aimed to construct surrogate models for predicting protein aggregation via data-driven methods using two types of databases. First, an aggregation propensity score database was constructed by calculating the scores for protein structures in the Protein Data Bank using Aggrescan3D 2.0. Moreover, feature- and graph-based models for predicting protein aggregation have been developed by using this database. The graph-based model outperformed the feature-based model, resulting in an R2 of 0.95, although it intrinsically required protein structures. Second, for the experimental data, a feature-based model was built using the Curated Protein Aggregation Database 2.0 to predict the aggregated intensity curves. In summary, this study suggests approaches that are more effective in predicting protein aggregation, depending on the type of descriptor and the database.
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Affiliation(s)
- Seungpyo Kang
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Minseon Kim
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Jiwon Sun
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Myeonghun Lee
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Kyoungmin Min
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
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Ishwarlall TZ, Adeleke VT, Maharaj L, Okpeku M, Adeniyi AA, Adeleke MA. Multi-epitope vaccine candidates based on mycobacterial membrane protein large (MmpL) proteins against Mycobacterium ulcerans. Open Biol 2023; 13:230330. [PMID: 37935359 PMCID: PMC10645115 DOI: 10.1098/rsob.230330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/26/2023] [Indexed: 11/09/2023] Open
Abstract
Buruli ulcer (BU) is a neglected tropical disease. It is caused by the bacterium Mycobacterium ulcerans and is characterized by skin lesions. Several studies were performed testing the Bacillus Calmette-Guérin (BCG) vaccine in human and animal models and M. ulcerans-specific vaccines in animal models. However, there are currently no clinically accepted vaccines to prevent M. ulcerans infection. The aim of this study was to identify T-cell and B-cell epitopes from the mycobacterial membrane protein large (MmpL) proteins of M. ulcerans. These epitopes were analysed for properties including antigenicity, immunogenicity, non-allergenicity, non-toxicity, population coverage and the potential to induce cytokines. The final 8 CD8+, 12 CD4+ T-cell and 5 B-cell epitopes were antigenic, non-allergenic and non-toxic. The estimated global population coverage of the CD8+ and CD4+ epitopes was 97.71%. These epitopes were used to construct five multi-epitope vaccine constructs with different adjuvants and linker combinations. The constructs underwent further structural analyses and refinement. The constructs were then docked with Toll-like receptors. Three of the successfully docked complexes were structurally analysed. Two of the docked complexes successfully underwent molecular dynamics simulations (MDS) and post-MDS analysis. The complexes generated were found to be stable. However, experimental validation of the complexes is required.
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Affiliation(s)
- Tamara Z. Ishwarlall
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Victoria T. Adeleke
- Department of Chemical Engineering, Mangosuthu University of Technology, Umlazi, Durban, South Africa
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Adebayo A. Adeniyi
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
- Department of Industrial Chemistry, Federal University Oye Ekiti, Ekiti State, Nigeria
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
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Debroy B, De A, Bhattacharya S, Pal K. In silico screening of herbal phytochemicals to develop a Rasayana for immunity against Nipah virus. J Ayurveda Integr Med 2023; 14:100825. [PMID: 38048723 PMCID: PMC10746367 DOI: 10.1016/j.jaim.2023.100825] [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: 12/30/2022] [Revised: 09/09/2023] [Accepted: 10/27/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND The first emergence of the Nipah virus (NiV) in 1998 from Malaysia became a major concern when it came to light and resurfaced on different occasions thereafter. NiV is a bat-borne zoonotic and pleomorphic virus that causes severe infection in human and animal hosts. Studies revealed fruit bats are the major reservoirs as natural hosts and pigs as intermediate hosts for the spread of this infection. This became a major concern as the disease was characterized by high pathogenicity varying from 40% to 80% depending on its acuteness. Moreover, the solemnity lies in the fact that the infection transcends from being a mere mild illness to an acute respiratory infection leading to fatal encephalitis with a reportedly high mortality rate. Currently, there is no treatment or vaccine available against the NiV. Many antiviral drugs have been explored and developed but with limited efficacy. METHODOLOGY In search of high-affinity ayurvedic alternatives, we conducted a pan-proteome in silico exploration of the NiV proteins for their interaction with the best-suited phytoconstituents. The toxicity prediction of thirty phytochemicals based on their LD50 value identified thirteen potential candidates. Molecular docking studies of those thirteen phytochemicals with five important NiV proteins identified Tanshinone I as the potential compound with a high binding affinity. RESULTS The pharmacokinetics and pharmacodynamics studies also aided in determining the absorption, distribution, metabolism, excretion, and toxicity of the selected phytoconstituent. Interestingly, docking studies also revealed Rosmariquinone as a potent alternative to the antiviral drug Remdesivir binding the same pocket of RNA-dependent RNA polymerase of the NiV. A molecular dynamics simulation study of the surface glycoprotein of NiV against Tanshinone I showed a stable complex formation and significant allosteric changes in the protein structure, implying that these phytochemicals could be a natural alternative to synthetic drugs against NiV. CONCLUSION This study provides preliminary evidence based on in silico analysis that the herbal molecules showed an effect against NiV. However, it is essential to further evaluate the efficacy of this approach through cell-based experiments, organoid models, and eventually clinical trials.
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Affiliation(s)
- Bishal Debroy
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India
| | - Arkajit De
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India
| | - Somdatta Bhattacharya
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India
| | - Kuntal Pal
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Barasat-Barrackpore Road, Kolkata, West Bengal, 700126, India; School of Biosciences and Technology (SBST), Vellore Institute Technology, Vellore, Tamil Nadu, 632014, India.
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Huang SM, Hsieh CY, Ting JU, De Castro-Cruz KA, Wang CC, Lee CJ, Tsai PW. Anti-COVID-19, Anti-Inflammatory, and Anti-Osteoarthritis Activities of Sesamin from Sesamum indicum L. Bioengineering (Basel) 2023; 10:1263. [PMID: 38002386 PMCID: PMC10669907 DOI: 10.3390/bioengineering10111263] [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: 09/07/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
During the COVID-19 (coronavirus disease 2019) outbreak, many people were infected, and the symptoms may persist for several weeks or months for recovering patients. This is also known as "long COVID" and includes symptoms such as fatigue, joint pain, muscle pain, et cetera. The COVID-19 virus may trigger hyper-inflammation associated with cytokine levels in the body. COVID-19 can trigger inflammation in the joints, which can lead to osteoarthritis (OA), while long-term COVID-19 symptoms may lead to joint damage and other inflammation problems. According to several studies, sesame has potent anti-inflammatory properties due to its major constituent, sesamin. This study examined sesamin's anti-inflammatory, anti-osteoarthritis, and anti-COVID-19 effects. Moreover, in vivo and in vitro assays were used to determine sesamin's anti-inflammatory activity against the RAW264.7 and SW1353 cell lines. Sesamin had a dose-dependent effect (20 mg/kg) in a monoiodoacetic acid (MIA)-induced osteoarthritis rat model. Sesamin reduced paw swelling and joint discomfort. In addition, the findings indicated that sesamin suppressed the expression of iNOS (inducible nitric oxide synthase) and COX-2 (cyclooxygenase-2) in the RAW264.7 cell line within the concentration range of 6.25-50 μM. Furthermore, sesamin also had a suppressive effect on MMP (matrix metalloproteinase) expression in chondrocytes and the SW1353 cell line within the same concentration range of 6.25-50 μM. To examine the anti-viral activity, an in silico analysis was performed to evaluate sesamin's binding affinity with SARS-CoV-2 RdRp (severe acute respiratory syndrome coronavirus 2 RNA-dependent RNA polymerase) and human ACE2 (angiotensin-converting enzyme 2). Compared to the controls, sesamin exhibited strong binding affinities towards SARS-CoV-2 RdRp and human ACE2. Furthermore, sesamin had a higher binding affinity for the ACE2 target protein. This study suggests that sesamin shows potential anti-SARS-CoV-2 activity for drug development.
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Affiliation(s)
- Shu-Ming Huang
- Department of Nutrition, College of Medical and Health Care, Hungkuang University, Taichung 433, Taiwan;
- Department of Nutrition, Nantou Hospital of Ministry of Health and Welfare, Nantou 540, Taiwan
| | - Cheng-Yang Hsieh
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.H.); (C.-C.W.)
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Jasmine U. Ting
- Department of Chemistry, College of Science, De La Salle University, Metro Manila 1004, Philippines;
| | - Kathlia A. De Castro-Cruz
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Metro Manila 1002, Philippines;
| | - Ching-Chiung Wang
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.H.); (C.-C.W.)
- Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
- Orthopedics Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Chia-Jung Lee
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.H.); (C.-C.W.)
- Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
| | - Po-Wei Tsai
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan
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Ishaq Z, Zaheer T, Waseem M, Shahwar Awan H, Ullah N, AlAsmari AF, AlAsmari F, Ali A. Immunoinformatics aided designing of a next generation poly-epitope vaccine against uropathogenic Escherichia coli to combat urinary tract infections. J Biomol Struct Dyn 2023:1-21. [PMID: 37811774 DOI: 10.1080/07391102.2023.2266018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 09/27/2023] [Indexed: 10/10/2023]
Abstract
Urinary tract infections (UTIs) are the second most prevalent bacterial infections and uropathogenic Escherichia coli (UPEC) stands among the primary causative agents of UTIs. The usage of antibiotics is the routine therapy being used in various countries to treat UTIs but becoming ineffective because of increasing antibiotic resistance among UPEC strains. Thus, there must be the development of some alternative treatment strategies such as vaccine development against UPEC. In the following study, pan-genomics along with reverse vaccinology approaches is used under the framework of bioinformatics for the identification of core putative vaccine candidates, employing 307 UPEC genomes (complete and draft), available publicly. A total of nine T-cell epitopes (derived from B-cells) of both MHC classes (I and II), were prioritized among three potential protein candidates. These epitopes were then docked together by using linkers (GPGPG and AAY) and an adjuvant (Cholera Toxin B) to form a poly-valent vaccine construct. The chimeric vaccine construct was undergone by molecular modelling, further refinement and energy minimization. We predicted positive results of the vaccine construct in immune simulations with significantly high levels of immune cells. The protein-protein docking analysis of vaccine construct with toll-like receptors predicted efficient binding, which was further validated by molecular dynamics simulation of vaccine construct with TLR-2 and TLR-4 at 120 ns, resulting in stable complexes' conformation throughout the simulation run. Overall, the vaccine construct demonstrated positive antigenic response. In future, this chimeric vaccine construct or the identified epitopes could be experimentally validated for the development of UPEC vaccines against UTIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zaara Ishaq
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Tahreem Zaheer
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Maaz Waseem
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Hayeqa Shahwar Awan
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Shifa International Hospitals Ltd, Islamabad, Pakistan
| | - Nimat Ullah
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- NYU Langone Health, New York, United States
| | - Abdullah F AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fawaz AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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Guidolin D, Tortorella C, Marcoli M, Cervetto C, De Caro R, Maura G, Agnati LF. Modulation of Neuron and Astrocyte Dopamine Receptors via Receptor-Receptor Interactions. Pharmaceuticals (Basel) 2023; 16:1427. [PMID: 37895898 PMCID: PMC10610355 DOI: 10.3390/ph16101427] [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: 09/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Dopamine neurotransmission plays critical roles in regulating complex cognitive and behavioral processes including reward, motivation, reinforcement learning, and movement. Dopamine receptors are classified into five subtypes, widely distributed across the brain, including regions responsible for motor functions and specific areas related to cognitive and emotional functions. Dopamine also acts on astrocytes, which express dopamine receptors as well. The discovery of direct receptor-receptor interactions, leading to the formation of multimeric receptor complexes at the cell membrane and providing the cell decoding apparatus with flexible dynamics in terms of recognition and signal transduction, has expanded the knowledge of the G-protein-coupled receptor-mediated signaling processes. The purpose of this review article is to provide an overview of currently identified receptor complexes containing dopamine receptors and of their modulatory action on dopamine-mediated signaling between neurons and between neurons and astrocytes. Pharmacological possibilities offered by targeting receptor complexes in terms of addressing neuropsychiatric disorders associated with altered dopamine signaling will also be briefly discussed.
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Affiliation(s)
- Diego Guidolin
- Department of Neuroscience, University of Padova, 35122 Padova, Italy; (C.T.); (R.D.C.)
| | - Cinzia Tortorella
- Department of Neuroscience, University of Padova, 35122 Padova, Italy; (C.T.); (R.D.C.)
| | - Manuela Marcoli
- Department of Pharmacy, University of Genova, 16126 Genova, Italy; (M.M.); (C.C.); (G.M.)
| | - Chiara Cervetto
- Department of Pharmacy, University of Genova, 16126 Genova, Italy; (M.M.); (C.C.); (G.M.)
| | - Raffaele De Caro
- Department of Neuroscience, University of Padova, 35122 Padova, Italy; (C.T.); (R.D.C.)
| | - Guido Maura
- Department of Pharmacy, University of Genova, 16126 Genova, Italy; (M.M.); (C.C.); (G.M.)
| | - Luigi F. Agnati
- Department of Biomedical, Metabolic Sciences and Neuroscience, University of Modena and Reggio Emilia, 41121 Modena, Italy;
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Venkateswaran S, Manivannan HP, Francis AP, Veeraraghavan VP, R G, Sankaran K. Identification of Potential Phytochemical Inhibitors From Conium maculatum Targeting the Epidermal Growth Factor Receptor in Metastatic Colorectal Cancer via Molecular Docking Analysis. Cureus 2023; 15:e48000. [PMID: 38034159 PMCID: PMC10687488 DOI: 10.7759/cureus.48000] [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: 10/04/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Background Metastatic colorectal cancer (mCRC) continues to rank as the second deadliest cancer on the global scale. CRC diagnosed at metastatic (stage IV) makes treatment strategies more challenging. Even though there are numerous therapeutic options available, the side effects of these treatments threaten the human health. Therefore, we are in the phase of searching new molecules that are less harmful and cost-effective. The common source of many pharmaceutical medications is plants. This study focuses on virtually screening phytochemicals from Conium maculatum as potential inhibitors of the epidermal growth factor receptor (EGFR), a crucial target in cancer therapy. Methods and materials C. maculatum was selected due to its phytochemicals and prior indications of its anticancer properties. In silico investigations encompass druglikeness screening, pharmacokinetics assessment, molecular docking, toxicity prediction, molecular target screening, and molecular dynamics simulations. A comprehensive analysis led to the identification of promising lead compounds. Results A total of 25 compounds exhibited favorable pharmacokinetic and drug-like characteristics. Among them, 12 compounds displayed a high affinity for EGFR as determined by molecular docking experiments. Further safety assessment using ProTox-II revealed that seven compounds had no anticipated toxicity, affirming their safety profiles. Conclusion These findings collectively predicted the efficacy of seven phytochemicals from C. maculatum as EGFR inhibitors in mCRC. Further experimental investigations and optimization of the identified leads were needed to validate the efficacy and safety of identified lead compounds and explore their therapeutic potential in CRC.
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Affiliation(s)
- Samyuktha Venkateswaran
- Centre of Molecular Medicine and Diagnostics (COMManD) Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Hema Priya Manivannan
- Centre of Molecular Medicine and Diagnostics (COMManD) Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Arul Prakash Francis
- Centre of Molecular Medicine and Diagnostics (COMManD) Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD) Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Gayathri R
- Centre of Molecular Medicine and Diagnostics (COMManD) Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Kavitha Sankaran
- Centre of Molecular Medicine and Diagnostics (COMManD) Department of Biochemistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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Kumar G, Hazra JP, Sinha S. Disordered regions endow structural flexibility to shell proteins and function towards shell-enzyme interactions in 1,2-propanediol utilization microcompartment. J Biomol Struct Dyn 2023; 41:8891-8901. [PMID: 36318590 DOI: 10.1080/07391102.2022.2138552] [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: 07/12/2022] [Accepted: 10/16/2022] [Indexed: 11/07/2022]
Abstract
Intrinsically disordered regions in proteins have been functionally linked to the protein-protein interactions and genesis of several membraneless organelles. Depending on their residual makeup, hydrophobicity or charge distribution they may remain in extended form or may assume certain conformations upon biding to a partner protein or peptide. The present work investigates the distribution and potential roles of disordered regions in the integral proteins of 1,2-propanediol utilization microcompartments. We use bioinformatics tools to identify the probable disordered regions in the shell proteins and enzyme of the 1,2-propanediol utilization microcompartment. Using a combination of computational modelling and biochemical techniques we elucidate the role of disordered terminal regions of a major shell protein and enzyme. Our findings throw light on the importance of disordered regions in the self-assembly, providing flexibility to shell protein and mediating its interaction with a native enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
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Begum MN, Mahtarin R, Ahmed S, Shahriar I, Hossain SR, Mia MW, Qadri SS, Qadri F, Mannoor K, Akhteruzzaman S. Investigation of the impact of nonsynonymous mutations on thyroid peroxidase dimer. PLoS One 2023; 18:e0291386. [PMID: 37699049 PMCID: PMC10497151 DOI: 10.1371/journal.pone.0291386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
Congenital hypothyroidism is one of the most common preventable endocrine disorders associated with thyroid dysgenesis or dyshormonogenesis. Thyroid peroxidase (TPO) gene defect is mainly responsible for dyshormonogenesis; a defect in the thyroid hormone biosynthesis pathway. In Bangladesh, there is limited data regarding the genetic etiology of Congenital Hypothyroidism (CH). The present study investigates the impact of the detected mutations (p.Ala373Ser, and p.Thr725Pro) on the TPO dimer protein. We have performed sequential molecular docking of H2O2 and I- ligands with both monomers of TPO dimer to understand the iodination process in thyroid hormone biosynthesis. Understanding homodimer interactions at the atomic level is a critical challenge to elucidate their biological mechanisms of action. The docking results reveal that mutations in the dimer severely disrupt its catalytic interaction with essential ligands. Molecular dynamics simulation has been performed to validate the docking results, thus realizing the consequence of the mutation in the biological system's mimic. The dynamics results expose that mutations destabilize the TPO dimer protein. Finally, principal component analysis exhibits structural and energy profile discrepancies in wild-type and mutant dimers. The findings of this study highlight that the mutations in TPO protein can critically affect the dimer structure and loss of enzymatic activity is persistent. Other factors also might influence the hormone synthesis pathway, which is under investigation.
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Affiliation(s)
- Mst. Noorjahan Begum
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
- Virology Laboratory, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Rumana Mahtarin
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Sinthyia Ahmed
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Imrul Shahriar
- Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shekh Rezwan Hossain
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
| | - Md. Waseque Mia
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Syed Saleheen Qadri
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
| | - Firdausi Qadri
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
- Mucosal Immunology and Vaccinology, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Kaiissar Mannoor
- Institute for Developing Science and Health Initiatives (ideSHi), ECB Chattar, Mirpur, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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Maryami F, Rismani E, Davoudi-Dehaghani E, Khalesi N, Talebi S, Mahdian R, Zeinali S. In silico Analysis of Two Novel Variants in the Pyruvate Carboxylase (PC) Gene Associated with the Severe Form of PC Deficiency. IRANIAN BIOMEDICAL JOURNAL 2023; 27:307-19. [PMID: 37873728 PMCID: PMC10707810 DOI: 10.61186/ibj.27.5.307] [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: 04/08/2023] [Accepted: 06/17/2023] [Indexed: 12/17/2023]
Abstract
Background Inborne errors of metabolism are a common cause of neonatal death. This study evaluated the acute early-onset metabolic derangement and death in two unrelated neonates. Methods Whole-exome sequencing (WES), Sanger sequencing, homology modeling, and in silico bioinformatics analysis were employed to assess the effects of variants on protein structure and function. Results WES revealed a novel homozygous variant, p.G303Afs*40 and p.R156P, in the pyruvate carboxylase (PC) gene of each neonate, which both were confirmed by Sanger sequencing. Based on the American College of Medical Genetics and Genomics guidelines, the p.G303Afs*40 was likely pathogenic, and the p.R156P was a variant of uncertain significance (VUS). Nevertheless, a known variant at position 156, the p.R156Q, was also a VUS. Protein secondary structure prediction showed changes in p.R156P and p.R156Q variants compared to the wild-type protein. However, p.G303Afs*40 depicted significant changes at C-terminal. Furthermore, comparing the interaction of wild-type and variant proteins with the ATP ligand during simulations, revealed a decreased affinity to the ATP in all the variants. Moreover, analysis of Single nucleotide polymorphism impacts on PC protein using Polyphen-2, SNAP2, FATHMM, and SNPs&GO servers predicted both R156P and R156Q as damaging variants. Likewise, free energy calculations demonstrated the destabilizing effect of both variants on PC. Conclusion This study confirmed the pathogenicity of both variants and suggested them as a cause of type B Pyruvate carboxylase deficiency. The results of this study would provide the family with prenatal diagnosis and expand the variant spectrum in the PC gene,which is beneficial for geneticists and endocrinologists.
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Affiliation(s)
- Fereshteh Maryami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Rismani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Nasrin Khalesi
- Department of Pediatrics and Neonatal Intensive Care Unit, Ali-Asghar Children’s Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Reza Mahdian
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
- Kawsar Human Genetics Research Center, Tehran, Iran
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37
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Bhowmik D, Bhuyan A, Gunalan S, Kothandan G, Kumar D. In silico and immunoinformatics based multiepitope subunit vaccine design for protection against visceral leishmaniasis. J Biomol Struct Dyn 2023:1-22. [PMID: 37655736 DOI: 10.1080/07391102.2023.2252901] [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: 02/12/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
Visceral leishmaniasis (VL) is a vector-borne neglected tropical protozoan disease with high fatality and no certified vaccine. Conventional vaccine preparation is challenging and tedious. Here in this work, we created a global multiepitope subunit vaccination against VL utilizing innovative immunoinformatics technique based on the extensively conserved epitopic regions of the PrimPol protein of Leishmania donovani consisting of four subunits which were analyzed and studied, out of which DNA primase large subunit and DNA polymerase α subunit B were evaluated as antigens by Vaxijen 2.0. The multiepitope vaccine design includes a single adjuvant β-defensins, eight CTL epitopes, eight HTL epitopes, seven linear BCL epitopes and one discontinuous BCL epitope to induce innate, cellular and humoral immune responses against VL. The Expasy ProtParam tool characterized the physiochemical parameters of the vaccine. At the same time, SOLpro evaluated our vaccine constructs to be soluble upon expression. We also modeled the stable tertiary structure of our vaccine construct through Robetta modeling for molecular docking studies with toll-like receptor proteins through HADDOCK 2.4. Simulations based on molecular dynamics revealed an intact vaccine and TLR8 complex, supporting our vaccine design's immunogenicity. Also, the immune simulation of our vaccine by the C-ImmSim server demonstrated the potency of the multiepitope vaccine construct to induce proper immune response for host defense. Codon optimization and in silico cloning of our vaccine further assured high expression. The outcomes of our study on multiepitope vaccine design significantly produced a potential candidate against VL and can potentially eradicate the disease in the future after clinical investigations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deep Bhowmik
- Deparment of Microbiology, Assam University, Silchar, Assam, India
| | - Achyut Bhuyan
- Deparment of Microbiology, Assam University, Silchar, Assam, India
| | - Seshan Gunalan
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, India
| | - Gugan Kothandan
- Biopolymer Modelling Laboratory, Centre of Advanced Study in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, India
| | - Diwakar Kumar
- Deparment of Microbiology, Assam University, Silchar, Assam, India
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Ahmed Al-Madhagi H. Computational Identification of Most Deleterious Missense Mutations in Human PD-1 Gene. ScientificWorldJournal 2023; 2023:4360203. [PMID: 37583448 PMCID: PMC10425257 DOI: 10.1155/2023/4360203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/22/2023] [Accepted: 07/27/2023] [Indexed: 08/17/2023] Open
Abstract
Traditional cancer treatment approaches are often hindered by the presence of toxic side effects and the high rate of relapse observed in treated organs. In contrast, novel immunotherapeutic strategies targeting immune checkpoint inhibitors, particularly PD-1, have demonstrated promising results with minimal adverse effects. However, the emergence of immunotherapeutic-resistant tumors, predominantly caused by intrinsic mutations, poses a significant obstacle to successful treatment outcomes. Consequently, the primary objective of this study was to screen for the most detrimental missense mutations in the PD-1 gene associated with immunotherapeutic resistance. To achieve this aim, a comprehensive screening process utilizing 20 web servers, incorporating both sequence- and structure-based methodologies, was undertaken. Through meticulous analysis and mutual disease association sorting, four specific missense mutations were successfully identified. These mutations, namely, R38C, D61V, R94C, and D117V, emerged as the leading contributors to genetic cancer progression and immunotherapeutic resistance against PD-1 blockers. The findings presented in this study are supported by multiple lines of evidence. A thorough examination of protein topology, structural alignment, docking interactions with PD-L1, and protein flexibility collectively confirmed the pathogenic nature of these sorted mutations. By considering these various aspects, we have gained a comprehensive understanding of the underlying mechanisms driving immunotherapeutic resistance. In conclusion, the comprehensive screening process undertaken in this study has successfully identified R38C, D61V, R94C, and D117V as the primary mutations contributing to genetic cancer progression and immunotherapeutic resistance against PD-1 blockers. The integration of protein topology analysis, structural alignment, docking studies with PD-L1, and assessment of protein flexibility have collectively provided robust evidence to support the pathogenic significance of these mutations.
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Cho HJ, Gurbuz F, Stamou M, Kotan LD, Farmer SM, Can S, Tompkins MF, Mammadova J, Altincik SA, Gokce C, Catli G, Bugrul F, Bartlett K, Turan I, Balasubramanian R, Yuksel B, Seminara SB, Wray S, Topaloglu AK. POU6F2 mutation in humans with pubertal failure alters GnRH transcript expression. Front Endocrinol (Lausanne) 2023; 14:1203542. [PMID: 37600690 PMCID: PMC10436210 DOI: 10.3389/fendo.2023.1203542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/22/2023] Open
Abstract
Idiopathic hypogonadotropic hypogonadism (IHH) is characterized by the absence of pubertal development and subsequent impaired fertility often due to gonadotropin-releasing hormone (GnRH) deficits. Exome sequencing of two independent cohorts of IHH patients identified 12 rare missense variants in POU6F2 in 15 patients. POU6F2 encodes two distinct isoforms. In the adult mouse, expression of both isoform1 and isoform2 was detected in the brain, pituitary, and gonads. However, only isoform1 was detected in mouse primary GnRH cells and three immortalized GnRH cell lines, two mouse and one human. To date, the function of isoform2 has been verified as a transcription factor, while the function of isoform1 has been unknown. In the present report, bioinformatics and cell assays on a human-derived GnRH cell line reveal a novel function for isoform1, demonstrating it can act as a transcriptional regulator, decreasing GNRH1 expression. In addition, the impact of the two most prevalent POU6F2 variants, identified in five IHH patients, that were located at/or close to the DNA-binding domain was examined. Notably, one of these mutations prevented the repression of GnRH transcripts by isoform1. Normally, GnRH transcription increases as GnRH cells mature as they near migrate into the brain. Augmentation earlier during development can disrupt normal GnRH cell migration, consistent with some POU6F2 variants contributing to the IHH pathogenesis.
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Affiliation(s)
- Hyun-Ju Cho
- Cellular and Developmental Neurobiology Section, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Fatih Gurbuz
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Türkiye
| | - Maria Stamou
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Leman Damla Kotan
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Türkiye
| | - Stephen Matthew Farmer
- Cellular and Developmental Neurobiology Section, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Sule Can
- Division of Pediatric Endocrinology, İzmir Tepecik Training and Research Hospital, Health Sciences University, İzmir, Türkiye
| | - Miranda Faith Tompkins
- Cellular and Developmental Neurobiology Section, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Jamala Mammadova
- Division of Pediatric Endocrinology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Türkiye
| | - S. Ayca Altincik
- Division of Pediatric Endocrinology, Faculty of Medicine, Pamukkale University, Denizli, Türkiye
| | - Cumali Gokce
- Division of Endocrinology, Faculty of Medicine, Mustafa Kemal University, Hatay, Türkiye
| | - Gonul Catli
- Division of Pediatric Endocrinology, İzmir Tepecik Training and Research Hospital, Health Sciences University, İzmir, Türkiye
| | - Fuat Bugrul
- Division of Pediatric Endocrinology, Faculty of Medicine, Selcuk University, Konya, Türkiye
| | - Keenan Bartlett
- Cellular and Developmental Neurobiology Section, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Ihsan Turan
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Türkiye
| | - Ravikumar Balasubramanian
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Bilgin Yuksel
- Division of Pediatric Endocrinology, Faculty of Medicine, Cukurova University, Adana, Türkiye
| | - Stephanie B. Seminara
- Harvard Reproductive Sciences Center, The Reproductive Endocrine Unit and The Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Susan Wray
- Cellular and Developmental Neurobiology Section, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - A. Kemal Topaloglu
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Mississippi Medical Center, Jackson, MS, United States
- Division of Pediatric Endocrinology, Massachusetts General Hospital for Children and Harvard Medical School, Boston, MS, United States
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40
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Dutta Gupta O, Karbat I, Pal K. Understanding the Molecular Regulation of Serotonin Receptor 5-HTR 1B-β-Arrestin1 Complex in Stress and Anxiety Disorders. J Mol Neurosci 2023; 73:664-677. [PMID: 37580644 DOI: 10.1007/s12031-023-02146-7] [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: 01/18/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
The serotonin receptor subtype 5-HTR1B is widely distributed in the brain with an important role in various behavioral implications including neurological conditions and psychiatric disorders. The neuromodulatory action of 5-HTR1B largely depends upon its arrestin mediated signaling pathway. In this study, we tried to investigate the role of unusually long intracellular loop 3 (ICL3) region of the serotonin receptor 5-HTR1B in interaction with β-arrestin1 (Arr2) to compensate for the absence of the long cytoplasmic tail. Molecular modeling and docking tools were employed to obtain a suitable molecular conformation of the ICL3 region in complex with Arr2 which dictates the specific complex formation of 5-HTR1B with Arr2. This reveals the novel molecular mechanism of phosphorylated ICL3 mediated GPCR-arrestin interaction in the absence of the long cytoplasmic tail. The in-cell disulfide cross-linking experiments and molecular dynamics simulations of the complex further validate the model of 5-HTR1B-ICL3-Arr2 complex. Two serine residues (Ser281 and Ser295) within the 5-HTR1B-ICL3 region were found to be occupying the electropositive pocket of Arr2 in our model and might be crucial for phosphorylation and specific Arr2 binding. The alignment studies of these residues showed them to be conserved only across 5-HTR1B mammalian species. Thus, our studies were able to predict a molecular conformation of 5-HTR1B-Arr2 and identify the role of long ICL3 in the signaling process which might be crucial in designing targeted drugs (biased agonists) that promote GPCR-Arr2 signaling to deter the effects of stress and anxiety-like disorders.
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Affiliation(s)
- Oindrilla Dutta Gupta
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, 700126, Kolkata, West Bengal, India
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Kuntal Pal
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, 700126, Kolkata, West Bengal, India.
- School of Biosciences and Technology (SBST), Vellore Institute of Technology, 632014, Vellore, Tamil Nadu, India.
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De Toni L, Cosci I, Sabovic I, Di Nisio A, Guidolin D, Pedrucci F, Finocchi F, Dall'Acqua S, Foresta C, Ferlin A, Garolla A. Membrane Cholesterol Inhibits Progesterone-Mediated Sperm Function through the Possible Involvement of ABHD2. Int J Mol Sci 2023; 24:ijms24119254. [PMID: 37298205 DOI: 10.3390/ijms24119254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Abhydrolase domain containing 2-acylglycerol lipase (ABHD2) was recently claimed as the membrane receptor of progesterone (P4) in sperm cells, mediating cell processes such as sperm chemotaxis and acrosome reaction. Here, we investigated the role of membrane cholesterol (Chol) on ABHD2-mediated human sperm chemotaxis. Human sperm cells were obtained from twelve normozoospemic healthy donors. ABHD2-Chol interaction was modelled by computational molecular-modelling (MM). Sperm membrane Chol content was depleted by incubating cells with cyclodextrin (CD) or augmented by the incubation with the complex between CD and Chol (CD:Chol). Cell Chol levels were quantified by liquid chromatography-mass spectrometry. Sperm migration upon P4 gradient was evaluated through the accumulation assay in a specific migration device. Motility parameters were evaluated by sperm class analyzer, whilst intracellular calcium concentration, acrosome reaction and mitochondrial membrane potential were evaluated with calcium orange, FITC-conjugated anti-CD46 antibody and JC-1 fluorescent probes, respectively. MM analysis showed the possible stable binding Chol to ABHD2, resulting in to major impact on the protein backbone flexibility. The treatment with CD was associated with a dose-dependent increase in sperm migration in a 160 nM P4 gradient, together with increase in sperm motility parameters and levels of acrosome reaction. The treatment with CD:Chol was associated with essentially opposite effects. Chol was, thus, suggested to inhibit P4-mediated sperm function through the possible inhibition of ABHD2.
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Affiliation(s)
- Luca De Toni
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, 35128 Padova, Italy
| | - Ilaria Cosci
- Veneto Institute of Oncology IOV-IRCCS, 35128 Padova, Italy
| | - Iva Sabovic
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, 35128 Padova, Italy
| | - Andrea Di Nisio
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, 35128 Padova, Italy
| | - Diego Guidolin
- Department of Neuroscience, Section of Anatomy, University of Padova, 35128 Padova, Italy
| | - Federica Pedrucci
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, 35128 Padova, Italy
| | - Federica Finocchi
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, 35128 Padova, Italy
| | - Stefano Dall'Acqua
- Department of Pharmaceutical Science, University of Padova, 35128 Padova, Italy
| | - Carlo Foresta
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, 35128 Padova, Italy
| | - Alberto Ferlin
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, 35128 Padova, Italy
| | - Andrea Garolla
- Department of Medicine, Unit of Andrology and Reproductive Medicine, University of Padova, 35128 Padova, Italy
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Das S, Dey A, Maji S, Sahoo A, Barman A, Santra S, Mondal S, Mondal KC, Chattopadhyay S. Attenuation of fluoride-induced hepatorenal oxidative stress by ferulic acid in vivo: An approach with in-silico analysis and interaction informatics of ferulic acid. J Trace Elem Med Biol 2023; 77:127133. [PMID: 36638706 DOI: 10.1016/j.jtemb.2023.127133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/11/2023]
Abstract
BACKGROUND Chronic fluoride toxicity induces oxidative strain and lipid peroxidation and imparts deleterious effects on human metabolic organs. AIM The present study aimed to expose the defensive impact of ferulic acid against sodium fluoride (NaF) induced hepatorenal dysfunction at the biochemical and antioxidative systems. METHODS In-vivo. Rats were arbitrarily separated into five groups as control, sodium fluoride-treated (200 ppm kg -1), vitamin C -as a positive control, and FA co-administered groups with 10 mg kg -1 and 20 mg kg -1 body weight for 56 days. In the present investigation, we measured antioxidant enzymes, superoxide dismutase, catalase, and lactate dehydrogenase by electrozymographic and spectrophotometric methods. Biochemical assessment of TBARS, conjugated diene, and different serum biomarkers was done for liver and kidney functionality tests. In-silico. An in-silico study was conducted through a molecular docking experiment to evaluate the binding potentiality of FA by employing AutoDock Vina [version 1.5.6] to overcome the abnormality in the activities of catalase, and superoxide dismutase in NaF promoted toxicity of hepatorenal system. In-vitro. An in vitro biochemical experiment was conducted to support the in-silico study. RESULTS Superoxide dismutase and catalase were decreased in the intoxicated rat. Ferulic acid (FA) as an antioxidant remarkably defended the NaF-mediated deterioration of the antioxidative status in the hepatorenal system, lowering lipid peroxidation products, malondialdehyde, and conjugated diene. Serum biomarkers, ALT, AST, ALP, urea, and creatinine increased in the intoxicated group than in control. Ferulic acid significantly neutralized the ill effects of NaF on serum lipid profile. In-silico analysis hypothesized the strong interaction of FA with the active side of catalase and superoxide dismutase that prevented the binding of NaF at the active site of these mentioned enzymes and this was further validated by in-vitro assay. CONCLUSION However, FA modulates free radical generation and protected these metabolic organs against sodium fluoride-induced injury.
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Affiliation(s)
- Seba Das
- Centre for Life Sciences, Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Arindam Dey
- Dept. of Biomedical Laboratory Science and Management and Clinical Nutrition and Dietetics Division (UGC Innovative Department), Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Shilpa Maji
- Dept. of Biomedical Laboratory Science and Management and Clinical Nutrition and Dietetics Division (UGC Innovative Department), Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Asim Sahoo
- Centre for Life Sciences, Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Ananya Barman
- Dept. of Biomedical Laboratory Science and Management and Clinical Nutrition and Dietetics Division (UGC Innovative Department), Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Sourav Santra
- Dept. of Microbiology, Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Subhadeep Mondal
- Centre for Life Sciences, Vidyasagar University, Midnapore 721102, West Bengal, India
| | | | - Sandip Chattopadhyay
- Centre for Life Sciences, Vidyasagar University, Midnapore 721102, West Bengal, India; Dept. of Biomedical Laboratory Science and Management and Clinical Nutrition and Dietetics Division (UGC Innovative Department), Vidyasagar University, Midnapore 721102, West Bengal, India.
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Papaleo E, Tiberti M, Arnaudi M, Pecorari C, Faienza F, Cantwell L, Degn K, Pacello F, Battistoni A, Lambrughi M, Filomeni G. TRAP1 S-nitrosylation as a model of population-shift mechanism to study the effects of nitric oxide on redox-sensitive oncoproteins. Cell Death Dis 2023; 14:284. [PMID: 37085483 PMCID: PMC10121659 DOI: 10.1038/s41419-023-05780-6] [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: 12/11/2022] [Revised: 03/13/2023] [Accepted: 03/27/2023] [Indexed: 04/23/2023]
Abstract
S-nitrosylation is a post-translational modification in which nitric oxide (NO) binds to the thiol group of cysteine, generating an S-nitrosothiol (SNO) adduct. S-nitrosylation has different physiological roles, and its alteration has also been linked to a growing list of pathologies, including cancer. SNO can affect the function and stability of different proteins, such as the mitochondrial chaperone TRAP1. Interestingly, the SNO site (C501) of TRAP1 is in the proximity of another cysteine (C527). This feature suggests that the S-nitrosylated C501 could engage in a disulfide bridge with C527 in TRAP1, resembling the well-known ability of S-nitrosylated cysteines to resolve in disulfide bridge with vicinal cysteines. We used enhanced sampling simulations and in-vitro biochemical assays to address the structural mechanisms induced by TRAP1 S-nitrosylation. We showed that the SNO site induces conformational changes in the proximal cysteine and favors conformations suitable for disulfide bridge formation. We explored 4172 known S-nitrosylated proteins using high-throughput structural analyses. Furthermore, we used a coarse-grained model for 44 protein targets to account for protein flexibility. This resulted in the identification of up to 1248 proximal cysteines, which could sense the redox state of the SNO site, opening new perspectives on the biological effects of redox switches. In addition, we devised two bioinformatic workflows ( https://github.com/ELELAB/SNO_investigation_pipelines ) to identify proximal or vicinal cysteines for a SNO site with accompanying structural annotations. Finally, we analyzed mutations in tumor suppressors or oncogenes in connection with the conformational switch induced by S-nitrosylation. We classified the variants as neutral, stabilizing, or destabilizing for the propensity to be S-nitrosylated and undergo the population-shift mechanism. The methods applied here provide a comprehensive toolkit for future high-throughput studies of new protein candidates, variant classification, and a rich data source for the research community in the NO field.
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Affiliation(s)
- Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark.
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark.
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Matteo Arnaudi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Chiara Pecorari
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Fiorella Faienza
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Lisa Cantwell
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Degn
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Francesca Pacello
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Battistoni
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
| | - Giuseppe Filomeni
- Redox Biology, Danish Cancer Society Research Center, 2100, Copenhagen, Denmark
- Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
- Center for Healthy Aging, Copenhagen University, 2200, Copenhagen, Denmark
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Lin CK, Chen BY, Ting JU, Rogio KGG, Tsai PW, Liu YC. Deciphering Houttuynia cordata extract as electron shuttles with anti-COVID-19 activity and its performance in microbial fuel cells. J Taiwan Inst Chem Eng 2023; 145:104838. [PMID: 37051508 PMCID: PMC10068517 DOI: 10.1016/j.jtice.2023.104838] [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: 02/10/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023]
Abstract
Background Traditional herbal medicines usually contain electron shuttle (ES)-like structures compounds which are potential candidates for antiviral compounds selection. Houttuynia cordata is applied as a biomaterial to decipher its potential applications in bioenergy extraction in microbial fuel cells (MFCs) and anti-COVID-19 via molecular docking evaluation. Methods H. cordata leaves extracts by water and 60% ethanol solvent were analyzed for total polyphenols, antioxidant activity, cyclic voltammetry (CV), and MFCs. The bioactive compounds of H. cordata leaves extracts were assayed via LC/MS analysis. Identification of the marker substances for potential antiviral activity using a molecular docking model was provided. Significant findings 60% ethanol extract exhibits the highest total polyphenols and antioxidant activity compared with water extracts. Bioenergy extraction in MFCs showed that 60% ethanol extracts could give 1.76-fold more power generation compared to the blank. Flavonoids and their sugar-to-glycan ratios increased after CV scanning and they are expected to be effective ES substances. Quercitrin, from the H. cordata extract that shares an ES-like structure, was found to exhibit strong binding affinities towards ACE2 and RdRp. This indicated the potential of H. cordata leaves as a promising antiviral herb.
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Affiliation(s)
- Chia-Kai Lin
- Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan
| | - Bor-Yann Chen
- Department of Chemical and Materials Engineering, National I-Lan University, I-Lan 260, Taiwan
| | - Jasmine U Ting
- Department of Chemistry, College of Science, De La Salle University, Metro Manila 1004, Philippines
| | - Kristian Gil G Rogio
- School of Chemical, Biological, and Materials Engineering and Sciences, Mapúa University, Metro Manila 1002, Philippines
| | - Po-Wei Tsai
- Department of Medical Science Industries, College of Health Sciences, Chang Jung Christian University, Tainan 711, Taiwan
| | - Yung-Chuan Liu
- Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan
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Jabin A, Uddin MF, Al Azad S, Rahman A, Tabassum F, Sarker P, Morshed AKMH, Rahman S, Raisa FF, Sakib MR, Olive AH, Islam T, Tahsin R, Ahmed SZ, Biswas P, Habiba MU, Siddiquy M, Jafary M. Target-specificity of different amyrin subunits in impeding HCV influx mechanism inside the human cells considering the quantum tunnel profiles and molecular strings of the CD81 receptor: a combined in silico and in vivo study. In Silico Pharmacol 2023; 11:8. [PMID: 36999133 PMCID: PMC10052254 DOI: 10.1007/s40203-023-00144-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/11/2023] [Indexed: 03/31/2023] Open
Abstract
HCV is a hepatotropic RNA virus recognized for its frequent virulence and fatality worldwide. Despite many vaccine development programs underway, researchers are on a quest for natural bioactive compounds due to their multivalent efficiencies against viral infections, considering which the current research aimed to figure out the target-specificity and therapeutic potentiality of α, β, and δ subunits of amyrin, as novel bioactive components against the HCV influx mechanism. Initially, the novelty of amyrin subunits was conducted from 203 pharmacophores, comparing their in-silico pharmacokinetic and pharmacodynamic profiles. Besides, the best active site of CD81 was determined following the quantum tunneling algorithm. The molecular dynamic simulation was conducted (100 ns) following the molecular docking steps to reveal the parameters- RMSD (Å); Cα; RMSF (Å); MolSA (Å2); Rg (nm); PSA (Å); SASA (Å2), and the MM-GBSA dG binding scores. Besides, molecular strings of CD81, along with the co-expressed genes, were classified, as responsible for encoding CD81-mediated protein clusters during HCV infection, resulting in the potentiality of amyrins as targeted prophylactics in HCV infection. Finally, in vivo profiling of the oxidative stress marker, liver-specific enzymes, and antioxidant markers was conducted in the DMN-induced mice model, where β-amyrin scored the most significant values in all aspects.
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Affiliation(s)
- Anika Jabin
- grid.443020.10000 0001 2295 3329Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Mohammad Fahim Uddin
- grid.413273.00000 0001 0574 8737College of Material Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang People’s Republic of China
| | - Salauddin Al Azad
- grid.258151.a0000 0001 0708 1323Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu Province People’s Republic of China
| | - Ashfaque Rahman
- grid.443020.10000 0001 2295 3329Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Fawzia Tabassum
- grid.412506.40000 0001 0689 2212Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Pritthy Sarker
- grid.443020.10000 0001 2295 3329Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - A K M Helal Morshed
- grid.207374.50000 0001 2189 3846Pathology and Pathophysiology Major, Academy of Medical Science, Zhengzhou University, Zhengzhou City, 450001 Henan Province People’s Republic of China
| | - Samiur Rahman
- grid.443020.10000 0001 2295 3329Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Fatima Fairuz Raisa
- grid.52681.380000 0001 0746 8691Department of Electrical and Electronic Engineering, Brac University, Dhaka, 1212 Bangladesh
| | - Musfiqur Rahman Sakib
- grid.449329.10000 0004 4683 9733Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100 Bangladesh
| | - Abeer Hasan Olive
- grid.442996.40000 0004 0451 6987Department of Pharmacy, East West University, Dhaka, 1212 Bangladesh
| | - Tabassum Islam
- grid.442996.40000 0004 0451 6987Department of Computer Science and Engineering, East West University, Dhaka, 1212 Bangladesh
| | - Ramisha Tahsin
- grid.443020.10000 0001 2295 3329Department of Pharmaceutical Sciences, North South University, Dhaka, 1229 Bangladesh
| | - Shahlaa Zernaz Ahmed
- grid.443020.10000 0001 2295 3329Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Mst. Umme Habiba
- Data Science Research Unit, RPG Interface Lab, Jashore, 7400 Bangladesh
| | - Mahbuba Siddiquy
- grid.258151.a0000 0001 0708 1323State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu Province People’s Republic of China
| | - Maryam Jafary
- grid.411705.60000 0001 0166 0922Division of Food Safety and Hygiene, Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, 1416634793 Iran
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Joshi A, Akhtar N, Sharma NR, Kaushik V, Borkotoky S. MERS virus spike protein HTL-epitopes selection and multi-epitope vaccine design using computational biology. J Biomol Struct Dyn 2023; 41:12464-12479. [PMID: 36935104 DOI: 10.1080/07391102.2023.2191137] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/03/2023] [Indexed: 03/20/2023]
Abstract
MERS-CoV, a zoonotic virus, poses a serious threat to public health globally. Thus, it is imperative to develop an effective vaccination strategy for protection against MERS-CoV. Immunoinformatics and computational biology tools provide a faster and more cost-effective strategy to design potential vaccine candidates. In this work, the spike proteins from different strains of MERS-CoV were selected to predict HTL-epitopes that show affinity for T-helper MHC-class II HTL allelic determinant (HLA-DRB1:0101). The antigenicity and conservation of these epitopes among the selected spike protein variants in different MERS-CoV strains were analyzed. The analysis identified five epitopes with high antigenicity: QSIFYRLNGVGITQQ, DTIKYYSIIPHSIRS, PEPITSLNTKYVAPQ, INGRLTTLNAFVAQQ and GDMYVYSAGHATGTT. Then, a multi-epitope vaccine candidate was designed using linkers and adjuvant molecules. Finally, the vaccine construct was subjected to molecular docking with TLR5 (Toll-like receptor-5). The proposed vaccine construct had strong binding energy of -32.3 kcal/mol when interacting with TLR5.Molecular dynamics simulation analysis showed that the complex of the vaccine construct and TLR5 is stable. Analysis using in silico immune simulation also showed that the prospective multi-epitope vaccine design had the potential to elicit a response within 70 days, with the immune system producing cytokines and immunoglobulins. Finally, codon adaptation and in silico cloning analysis showed that the candidate vaccine could be expressed in the Escherichia coli K12 strain. Here we also designed support vaccine construct MEV-2 by using B-cell and CD8+ CTL epitopes to generate the complete immunogenic effect. This study opens new avenues for the extension of research on MERS vaccine development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Joshi
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
- Department of Biochemistry, Kalinga University, Raipur, India
| | - Nahid Akhtar
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Neeta Raj Sharma
- Domain of Bioinformatics, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Vikas Kaushik
- Domain of Bioinformatics, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Subhomoi Borkotoky
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
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Santos J, Fernández Villamil SH, Delfino JM, Valsecchi WM. Structural differences between hypoxanthine phosphoribosyltransferase family members highlight opportunities for antiparasitic drug design in neglected diseases. Arch Biochem Biophys 2023; 737:109550. [PMID: 36796662 DOI: 10.1016/j.abb.2023.109550] [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: 12/21/2022] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 02/16/2023]
Abstract
Approaches to identify novel druggable targets for treating neglected diseases include computational studies that predict possible interactions of drugs and their molecular targets. Hypoxanthine phosphoribosyltransferase (HPRT) plays a central role in the purine salvage pathway. This enzyme is essential for the survival of the protozoan parasite T. cruzi, the causal agent of Chagas disease, and other parasites related to neglected diseases. Here we found dissimilar functional behaviours between TcHPRT and the human homologue, HsHPRT, in the presence of substrate analogues that can lie in differences in their oligomeric assemblies and structural features. To shed light on this issue, we carried out a comparative structural analysis between both enzymes. Our results show that HsHPRT is considerably more resistant to controlled proteolysis than TcHPRT. Moreover, we observed a variation in the length of two key loops depending on the structural arrangement of each protein (groups D1T1 and D1T1'). Such variations might be involved in inter-subunit communication or influencing the oligomeric state. Besides, to understand the molecular basis that govern D1T1 and D1T1' folding groups, we explored the distribution of charges on the interaction surfaces of TcHPRT and HsHPRT, respectively. To know whether the rigidity degree bears effect on the active site, we studied the flexibility of both proteins. The analysis performed here illuminates the underlying reasons and significance behind each protein's preference for one or the other quaternary arrangement that can be exploited for therapeutic approaches.
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Affiliation(s)
- J Santos
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - S H Fernández Villamil
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Argentina; Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Argentina
| | - J M Delfino
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Argentina
| | - W M Valsecchi
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA), Argentina.
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48
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Chen Z, Cui Y, Yao Y, Liu B, Yunis J, Gao X, Wang N, Cañete PF, Tuong ZK, Sun H, Wang H, Yang S, Wang R, Leong YA, Simon Davis D, Qin J, Liang K, Deng J, Wang CK, Huang YH, Roco JA, Nettelfield S, Zhu H, Xu H, Yu Z, Craik D, Liu Z, Qi H, Parish C, Yu D. Heparan sulfate regulates IL-21 bioavailability and signal strength that control germinal center B cell selection and differentiation. Sci Immunol 2023; 8:eadd1728. [PMID: 36800411 DOI: 10.1126/sciimmunol.add1728] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
In antibody responses, mutated germinal center B (BGC) cells are positively selected for reentry or differentiation. As the products from GCs, memory B cells and antibody-secreting cells (ASCs) support high-affinity and long-lasting immunity. Positive selection of BGC cells is controlled by signals received through the B cell receptor (BCR) and follicular helper T (TFH) cell-derived signals, in particular costimulation through CD40. Here, we demonstrate that the TFH cell effector cytokine interleukin-21 (IL-21) joins BCR and CD40 in supporting BGC selection and reveal that strong IL-21 signaling prioritizes ASC differentiation in vivo. BGC cells, compared with non-BGC cells, show significantly reduced IL-21 binding and attenuated signaling, which is mediated by low cellular heparan sulfate (HS) sulfation. Mechanistically, N-deacetylase and N-sulfotransferase 1 (Ndst1)-mediated N-sulfation of HS in B cells promotes IL-21 binding and signal strength. Ndst1 is down-regulated in BGC cells and up-regulated in ASC precursors, suggesting selective desensitization to IL-21 in BGC cells. Thus, specialized biochemical regulation of IL-21 bioavailability and signal strength sets a balance between the stringency and efficiency of GC selection.
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Affiliation(s)
- Zhian Chen
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Yanfang Cui
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, China
| | - Yin Yao
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Department of Otolaryngology-Head and Neck Surgery, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Liu
- Tsinghua-Peking Center for Life Sciences, Laboratory of Dynamic Immunobiology, School of Medicine, Tsinghua University, Beijing, China
| | - Joseph Yunis
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Xin Gao
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Naiqi Wang
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Pablo F Cañete
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Hongjian Sun
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Hao Wang
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Siling Yang
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Runli Wang
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Yew Ann Leong
- Centre for Inflammatory Diseases, Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - David Simon Davis
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Jiahuan Qin
- China-Australia Centre for Personalised Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaili Liang
- China-Australia Centre for Personalised Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Deng
- China-Australia Centre for Personalised Immunology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Conan K Wang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Queensland, Brisbane, QLD, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Jonathan A Roco
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Sam Nettelfield
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Huaming Zhu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Huajun Xu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
| | - Zhijia Yu
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - David Craik
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Queensland, Brisbane, QLD, Australia
| | - Zheng Liu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Hai Qi
- Tsinghua-Peking Center for Life Sciences, Laboratory of Dynamic Immunobiology, School of Medicine, Tsinghua University, Beijing, China
| | - Christopher Parish
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
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Hilpert C, Beranger L, Souza PCT, Vainikka PA, Nieto V, Marrink SJ, Monticelli L, Launay G. Facilitating CG Simulations with MAD: The MArtini Database Server. J Chem Inf Model 2023; 63:702-710. [PMID: 36656159 DOI: 10.1021/acs.jcim.2c01375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.
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Affiliation(s)
- Cécile Hilpert
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Louis Beranger
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Paulo C T Souza
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Petteri A Vainikka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Vincent Nieto
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Luca Monticelli
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
| | - Guillaume Launay
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), UMR 5086 CNRS & University of Lyon. 7 passage du Vercors, 69367 Lyon, France
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In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants. J Trop Med 2023. [DOI: 10.1155/2023/4771745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Despite the rigorous global efforts to control SARS-CoV-2 transmission, it continues to pose a serious threat to humans with the frequent emergence of new variants. Thus, robust therapeutics to combat the virus are a desperate need. The SARS-CoV-2 spike (S) protein is an important target protein as it mediates the entry of the virus inside the host cells, which is initiated by the binding of the receptor-binding domain (RBD) to its cognate receptor, angiotensin-converting enzyme 2 (ACE-2). Herein, the inhibition potential of several naturally occurring coumarins was investigated against the spike proteins of SARS-CoV-2 variants using computational approaches. Molecular docking studies revealed 26 coumarins with better binding energies than the reference ligands, molnupiravir and ceftazidime, against the S-RBD of the omicron variant. The top 10 best-docked coumarins were further analyzed to understand their binding interactions against the spike proteins of other variants (wild-type, Alpha, Beta, Gamma, and Delta), and these studies also demonstrated decent binding energies. Physicochemical, QSAR, and pharmacokinetics analyses of the coumarins revealed wedelolactone as the best inhibitor of the spike protein with ideal Lipinski’s drug-likeness and optimal ADMET properties. Furthermore, coarse-grained molecular dynamics (MD) simulation studies of spike protein-wedelolactone complexes validated the stable binding of wedelolactone in the respective binding pockets. As an outcome, wedelolactone could be utilized to develop a potent drug candidate against COVID-19 by blocking the viral entry into the host cell.
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