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Thakur S, Planeta Kepp K, Mehra R. Predicting virus Fitness: Towards a structure-based computational model. J Struct Biol 2023; 215:108042. [PMID: 37931730 DOI: 10.1016/j.jsb.2023.108042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogens. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼380,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India
| | - Kasper Planeta Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kongens Lyngby, Denmark
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India; Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Kutelabhata, Durg - 491001, Chhattisgarh, India.
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Gholami A. Alzheimer's disease: The role of proteins in formation, mechanisms, and new therapeutic approaches. Neurosci Lett 2023; 817:137532. [PMID: 37866702 DOI: 10.1016/j.neulet.2023.137532] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurological disorder that affects the central nervous system (CNS), leading to memory and cognitive decline. In AD, the brain experiences three main structural changes: a significant decrease in the quantity of neurons, the development of neurofibrillary tangles (NFT) composed of hyperphosphorylated tau protein, and the formation of amyloid beta (Aβ) or senile plaques, which are protein deposits found outside cells and surrounded by dystrophic neurites. Genetic studies have identified four genes associated with autosomal dominant or familial early-onset AD (FAD): amyloid precursor protein (APP), presenilin 1 (PS1), presenilin 2 (PS2), and apolipoprotein E (ApoE). The formation of plaques primarily involves the accumulation of Aβ, which can be influenced by mutations in APP, PS1, PS2, or ApoE genes. Mutations in the APP and presenilin (PS) proteins can cause an increased amyloid β peptides production, especially the further form of amyloidogenic known as Aβ42. Apart from genetic factors, environmental factors such as cytokines and neurotoxins may also have a significant impact on the development and progression of AD by influencing the formation of amyloid plaques and intracellular tangles. Exploring the causes and implications of protein aggregation in the brain could lead to innovative therapeutic approaches. Some promising therapy strategies that have reached the clinical stage include using acetylcholinesterase inhibitors, estrogen, nonsteroidal anti-inflammatory drugs (NSAIDs), antioxidants, and antiapoptotic agents. The most hopeful therapeutic strategies involve inhibiting activity of secretase and preventing the β-amyloid oligomers and fibrils formation, which are associated with the β-amyloid fibrils accumulation in AD. Additionally, immunotherapy development holds promise as a progressive therapeutic approach for treatment of AD. Recently, the two primary categories of brain stimulation techniques that have been studied for the treatment of AD are invasive brain stimulation (IBS) and non-invasive brain stimulation (NIBS). In this article, the amyloid proteins that play a significant role in the AD formation, the mechanism of disease formation as well as new drugs utilized to treat of AD will be reviewed.
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Affiliation(s)
- Amirreza Gholami
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
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De-Simone SG, Napoleão-Pêgo P, Gonçalves PS, Lechuga GC, Mandonado A, Graeff-Teixeira C, Provance DW. Angiostrongilus cantonensis an Atypical Presenilin: Epitope Mapping, Characterization, and Development of an ELISA Peptide Assay for Specific Diagnostic of Angiostrongyliasis. MEMBRANES 2022; 12:membranes12020108. [PMID: 35207030 PMCID: PMC8878667 DOI: 10.3390/membranes12020108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/10/2022]
Abstract
Background: Angiostrongyliasis, the leading cause universal of eosinophilic meningitis, is an emergent disease due to Angiostrongylus cantonensis (rat lungworm) larvae, transmitted accidentally to humans. The diagnosis of human angiostrongyliasis is based on epidemiologic characteristics, clinical symptoms, medical history, and laboratory findings, particularly hypereosinophilia in blood and cerebrospinal fluid. Thus, the diagnosis is difficult and often confused with those produced by other parasitic diseases. Therefore, the development of a fast and specific diagnostic test for angiostrongyliasis is a challenge mainly due to the lack of specificity of the described tests, and therefore, the characterization of a new target is required. Material and Methods: Using bioinformatics tools, the putative presenilin (PS) protein C7BVX5-1 was characterized structurally and phylogenetically. A peptide microarray approach was employed to identify single and specific epitopes, and tetrameric epitope peptides were synthesized to evaluate their performance in an ELISA-peptide assay. Results: The data showed that the A. cantonensis PS protein presents nine transmembrane domains, the catalytic aspartyl domain [(XD (aa 241) and GLGD (aa 332–335)], between TM6 and TM7 and the absence of the PALP and other characteristics domains of the class A22 and homologous presenilin (PSH). These individualities make it an atypical sub-branch of the PS family, located in a separate subgroup along with the enzyme Haemogonchus contournus and separated from other worm subclasses. Twelve B-linear epitopes were identified by microarray of peptides and validated by ELISA using infected rat sera. In addition, their diagnostic performance was demonstrated by an ELISA-MAP4 peptide. Conclusions: Our data show that the putative AgPS is an atypical multi-pass transmembrane protein and indicate that the protein is an excellent immunological target with two (PsAg3 and PsAg9) A. costarisencis cross-reactive epitopes and eight (PsAg1, PsAg2, PsAg6, PsAg7, PsAg8, PsAg10, PsAg11, PsAg12) apparent unique A. cantonensis epitopes. These epitopes could be used in engineered receptacle proteins to develop a specific immunological diagnostic assay for angiostrongyliasis caused by A. cantonensis.
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Affiliation(s)
- Salvatore G. De-Simone
- Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (P.S.G.); (G.C.L.); (D.W.P.J.)
- Laboratory of Epidemiology and Molecular Systematics (LESM), Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil
- Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24220-900, RJ, Brazil
- Correspondence:
| | - Paloma Napoleão-Pêgo
- Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (P.S.G.); (G.C.L.); (D.W.P.J.)
| | - Priscila S. Gonçalves
- Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (P.S.G.); (G.C.L.); (D.W.P.J.)
- Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24220-900, RJ, Brazil
| | - Guilherme C. Lechuga
- Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (P.S.G.); (G.C.L.); (D.W.P.J.)
| | - Arnaldo Mandonado
- Laboratory of Biology and Parasitology of Wild Mammals Reservoirs, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Carlos Graeff-Teixeira
- Infectious Diseases Unit, Department of Pathology, Federal University of Espirito Santo, Vitória 29075-910, ES, Brazil;
| | - David W. Provance
- Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), FIOCRUZ, Rio de Janeiro 21040-900, RJ, Brazil; (P.N.-P.); (P.S.G.); (G.C.L.); (D.W.P.J.)
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Chami M, Checler F. Alterations of the Endoplasmic Reticulum (ER) Calcium Signaling Molecular Components in Alzheimer's Disease. Cells 2020; 9:cells9122577. [PMID: 33271984 PMCID: PMC7760721 DOI: 10.3390/cells9122577] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023] Open
Abstract
Sustained imbalance in intracellular calcium (Ca2+) entry and clearance alters cellular integrity, ultimately leading to cellular homeostasis disequilibrium and cell death. Alzheimer’s disease (AD) is the most common cause of dementia. Beside the major pathological features associated with AD-linked toxic amyloid beta (Aβ) and hyperphosphorylated tau (p-tau), several studies suggested the contribution of altered Ca2+ handling in AD development. These studies documented physical or functional interactions of Aβ with several Ca2+ handling proteins located either at the plasma membrane or in intracellular organelles including the endoplasmic reticulum (ER), considered the major intracellular Ca2+ pool. In this review, we describe the cellular components of ER Ca2+ dysregulations likely responsible for AD. These include alterations of the inositol 1,4,5-trisphosphate receptors’ (IP3Rs) and ryanodine receptors’ (RyRs) expression and function, dysfunction of the sarco-endoplasmic reticulum Ca2+ ATPase (SERCA) activity and upregulation of its truncated isoform (S1T), as well as presenilin (PS1, PS2)-mediated ER Ca2+ leak/ER Ca2+ release potentiation. Finally, we highlight the functional consequences of alterations of these ER Ca2+ components in AD pathology and unravel the potential benefit of targeting ER Ca2+ homeostasis as a tool to alleviate AD pathogenesis.
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Affiliation(s)
- Mounia Chami
- Correspondence: ; Tel.: +33-4939-53457; Fax: +33-4939-53408
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