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Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 25301

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Prof. Dr. Salvatore G. De-Simone

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Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
Interests: microarray of peptides; chimeric proteins; diagnosis; emerging pathogens; target proteins
Special Issues, Collections and Topics in MDPI journals

Dr. Maria Izabel Florindo Guedes

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Department of Nutrition, State University of Ceara, Fortaleza 60714-903, Brazil
Interests: plant recombinant proteins; diagnostic; infectious diseases; vaccines

Special Issue Information

Dear Colleagues,

It is a great pleasure to invite you to contribute to this Special Issue entitled “Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases”. Recent epidemic outbreaks of emerging, re-emerging, and neglected infectious diseases have demonstrated the importance of applying control and prevention measures. For such actions to be practical, the development of methods resulting from the improvement of molecular biology, biochemistry, and cell biology has leveraged innovation. However, the interpretation of results requires different levels of knowledge so that the emergence of new technologies results in the development of new drugs, therapies, and more effective diagnoses. This Special Issue is open to all researchers, mainly from Brazil, studying emerging, re-emerging, and neglected infectious diseases at a molecular level. Original articles, as well as new perspectives or reviews on the matter, are welcome. Research in the fields of molecular studies in biology and chemistry, biochemistry of vaccines, molecular pathogenesis, genetic mutations, cloning and expression of proteins in plants and other systems, -omics, viral immunology, antiviral drugs, and tools to study these interactions at a molecular level are especially encouraged.

Prof. Dr. Salvatore G. De-Simone
Dr. Maria Izabel Florindo Guedes
Guest Editors

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Keywords

SARS-CoV
ZIKAV
host–parasite interaction
molecular diagnostics
molecular interactions
molecular pathogenesis
infectious diseases

Published Papers (11 papers)

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Editorial

Jump to: Research, Review

4 pages, 190 KiB

Open AccessEditorial

Recent Advances in Biochemistry and Molecular Biology of Infectious Diseases

by Salvatore Giovanni De-Simone

Int. J. Mol. Sci. 2023, 24(10), 8958; https://doi.org/10.3390/ijms24108958 - 18 May 2023

Viewed by 1301

Abstract

This Editorial highlights the various observations made in the Special Issue of the International Journal of Molecular Sciences on “Recent Advances in Biochemistry and Molecular Biology of Infectious Diseases” [...] Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

Research

Jump to: Editorial, Review

14 pages, 1569 KiB

Open AccessArticle

In Vitro Transcriptional Response of Eimeria tenella to Toltrazuril Reveals That Oxidative Stress and Autophagy Contribute to Its Anticoccidial Effect

by Lei Zhang, Hongtao Zhang, Shiqi Du, Xingju Song and Dandan Hu

Int. J. Mol. Sci. 2023, 24(9), 8370; https://doi.org/10.3390/ijms24098370 - 06 May 2023

Cited by 4 | Viewed by 1641

Abstract

Intestinal coccidiosis is a common parasitic disease in livestock, caused by the infection of Eimeria and Cystoisospora parasites, which results in great economic losses to animal husbandry. Triazine compounds, such as toltrazuril and diclazuril, are widely used in the treatment and chemoprophylaxis of coccidiosis. Unfortunately, widespread drug resistance has compromised their effectiveness. Most studies have focused on prophylaxis and therapeutics with toltrazuril in flocks, while a comprehensive understanding of how toltrazuril treatment alters the transcriptome of E. tenella remains unknown. In this study, merozoites of E. tenella were treated in vitro with 0.5 μg/mL toltrazuril for 0, 1, 2 and 4 h, respectively. The gene transcription profiles were then compared by high-throughput sequencing. Our results showed that protein hydrolysis genes were significantly upregulated after drug treatment, while cell cycle-related genes were significantly downregulated, suggesting that toltrazuril may affect parasite division. The expression of redox-related genes was upregulated and elevated levels of ROS and autophagosomes were detected in the parasite after toltrazuril treatment, suggesting that toltrazuril may cause oxidative stress to parasite cells and lead to its autophagy. Our results provide basic knowledge of the response of Eimeria genes to toltrazuril and further analysis of the identified transcriptional changes can provide useful information for a better understanding of the mechanism of action of toltrazuril against Eimeria. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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9 pages, 1733 KiB

Open AccessArticle

Lymphocyte-to-C-Reactive Protein (LCR) Ratio Is Not Accurate to Predict Severity and Mortality in Patients with COVID-19 Admitted to the ED

by Laure Abensur Vuillaume, François Lefebvre, Axel Benhamed, Amandine Schnee, Mathieu Hoffmann, Fernanda Godoy Falcao, Nathan Haber, Jonathan Sabah, Charles-Eric Lavoignet and Pierrick Le Borgne

Int. J. Mol. Sci. 2023, 24(6), 5996; https://doi.org/10.3390/ijms24065996 - 22 Mar 2023

Cited by 2 | Viewed by 1520

Abstract

Health care systems worldwide have been battling the ongoing COVID-19 pandemic. Since the beginning of the COVID-19 pandemic, Lymphocytes and CRP have been reported as markers of interest. We chose to investigate the prognostic value of the LCR ratio as a marker of severity and mortality in COVID-19 infection. Between 1 March and 30 April 2020, we conducted a multicenter, retrospective cohort study of patients with moderate and severe coronavirus disease 19 (COVID-19), all of whom were hospitalized after being admitted to the Emergency Department (ED). We conducted our study in six major hospitals of northeast France, one of the outbreak’s epicenters in Europe. A total of 1035 patients with COVID-19 were included in our study. Around three-quarters of them (76.2%) presented a moderate form of the disease, while the remaining quarter (23.8%) presented a severe form requiring admission to the ICU. At ED admission, the median LCR was significantly lower in the group presenting severe disease compared to that with moderate disease (versus 6.24 (3.24–12) versus 12.63 ((6.05–31.67)), p < 0.001). However, LCR was neither associated with disease severity (OR: 0.99, CI 95% (0.99–1)), p = 0.476) nor mortality (OR: 0.99, CI 95% (0.99–1)). In the ED, LCR, although modest, with a threshold of 12.63, was a predictive marker for severe forms of COVID-19. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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15 pages, 1489 KiB

Open AccessArticle

A New Strategy for Mapping Epitopes of LACK and PEPCK Proteins of Leishmania amazonensis Specific for Major Histocompatibility Complex Class I

by Edlainne Pinheiro Ferreira-Sena, Daiana de Jesus Hardoim, Flavia de Oliveira Cardoso, Luiz Ney d’Escoffier, Isabela Ferreira Soares, João Pedro Rangel da Silva Carvalho, Ricardo Almir Angnes, Stenio Perdigão Fragoso, Carlos Roberto Alves, Salvatore Giovanni De-Simone, Josué da Costa Lima-Junior, Alvaro Luiz Bertho, Tânia Zaverucha-do-Valle, Franklin Souza da Silva and Kátia da Silva Calabrese

Int. J. Mol. Sci. 2023, 24(6), 5972; https://doi.org/10.3390/ijms24065972 - 22 Mar 2023

Cited by 4 | Viewed by 1427

Abstract

Leishmaniasis represents a complex of diseases with a broad clinical spectrum and epidemiological diversity, considered a major public health problem. Although there is treatment, there are still no vaccines for cutaneous leishmaniasis. Because Leishmania spp. is an intracellular protozoan with several escape mechanisms, a vaccine must provoke cellular and humoral immune responses. Previously, we identified the Leishmania homolog of receptors for activated C kinase (LACK) and phosphoenolpyruvate carboxykinase (PEPCK) proteins as strong immunogens and candidates for the development of a vaccine strategy. The present work focuses on the in silico prediction and characterization of antigenic epitopes that might interact with mice or human major histocompatibility complex class I. After immunogenicity prediction on the Immune Epitope Database (IEDB) and the Database of MHC Ligands and Peptide Motifs (SYFPEITHI), 26 peptides were selected for interaction assays with infected mouse lymphocytes by flow cytometry and ELISpot. This strategy identified nine antigenic peptides (pL1-H2, pPL3-H2, pL10-HLA, pP13-H2, pP14-H2, pP15-H2, pP16-H2, pP17-H2, pP18-H2, pP26-HLA), which are strong candidates for developing a peptide vaccine against leishmaniasis. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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8 pages, 961 KiB

Open AccessCommunication

Comparison of SARS-CoV-2 Detection in Nasopharyngeal Swab and Saliva Samples from Patients Infected with Omicron Variant

by Licia Bordi, Giuseppe Sberna, Eleonora Lalle, Lavinia Fabeni, Valentina Mazzotta, Simone Lanini, Angela Corpolongo, Anna Rosa Garbuglia, Emanuele Nicastri, Enrico Girardi, Francesco Vaia, Andrea Antinori and Fabrizio Maggi

Int. J. Mol. Sci. 2023, 24(5), 4847; https://doi.org/10.3390/ijms24054847 - 02 Mar 2023

Cited by 4 | Viewed by 1349

Abstract

To compare the detection of the SARS-CoV-2 Omicron variant in nasopharyngeal-swab (NPS) and oral saliva samples. 255 samples were obtained from 85 Omicron-infected patients. SARS-CoV-2 load was measured in the NPS and saliva samples by using Simplexa™ COVID-19 direct and Alinity m SARS-CoV-2 AMP assays. Results obtained with the two diagnostic platforms showed very good inter-assay concordance (91.4 and 82.4% for saliva and NPS samples, respectively) and a significant correlation among cycle threshold (Ct) values. Both platforms revealed a highly significant correlation among Ct obtained in the two matrices. Although the median Ct value was lower in NPS than in saliva samples, the Ct drop was comparable in size for both types of samples after 7 days of antiviral treatment of the Omicron-infected patients. Our result demonstrates that the detection of the SARS-CoV-2 Omicron variant is not influenced by the type of sample used for PCR analysis, and that saliva can be used as an alternative specimen for detection and follow-up of Omicron-infected patients. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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14 pages, 3695 KiB

Open AccessArticle

Development of a Propidium Monoazide-Based Viability Quantitative PCR Assay for Red Sea Bream Iridovirus Detection

by Kyung-Ho Kim, Gyoungsik Kang, Won-Sik Woo, Min-Young Sohn, Ha-Jeong Son and Chan-Il Park

Int. J. Mol. Sci. 2023, 24(4), 3426; https://doi.org/10.3390/ijms24043426 - 08 Feb 2023

Cited by 2 | Viewed by 1640

Abstract

Red sea bream iridovirus (RSIV) is an important aquatic virus that causes high mortality in marine fish. RSIV infection mainly spreads through horizontal transmission via seawater, and its early detection could help prevent disease outbreaks. Although quantitative PCR (qPCR) is a sensitive and rapid method for detecting RSIV, it cannot differentiate between infectious and inactive viruses. Here, we aimed to develop a viability qPCR assay based on propidium monoazide (PMAxx), which is a photoactive dye that penetrates damaged viral particles and binds to viral DNA to prevent qPCR amplification, to distinguish between infectious and inactive viruses effectively. Our results demonstrated that PMAxx at 75 μM effectively inhibited the amplification of heat-inactivated RSIV in viability qPCR, allowing the discrimination of inactive and infectious RSIV. Furthermore, the PMAxx-based viability qPCR assay selectively detected the infectious RSIV in seawater more efficiently than the conventional qPCR and cell culture methods. The reported viability qPCR method will help prevent the overestimation of red sea bream iridoviral disease caused by RSIV. Furthermore, this non-invasive method will aid in establishing a disease prediction system and in epidemiological analysis using seawater. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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13 pages, 2040 KiB

Open AccessArticle

B-Cell Epitope Mapping of the Vibrio cholera Toxins A, B, and P and an ELISA Assay

by Salvatore G. De-Simone, Paloma Napoleão-Pêgo, Priscilla S. Gonçalves, Guilherme C. Lechuga, Sergian V. Cardoso, David W. Provance, Jr., Carlos M. Morel and Flavio R. da Silva

Int. J. Mol. Sci. 2023, 24(1), 531; https://doi.org/10.3390/ijms24010531 - 28 Dec 2022

Cited by 4 | Viewed by 1668

Abstract

Oral immunization with the choleric toxin (CT) elicits a high level of protection against its enterotoxin activities and can control cholera in endemic settings. However, the complete B-cell epitope map of the CT that is responsible for protection remains to be clarified. A library of one-hundred, twenty-two 15-mer peptides covering the entire sequence of the three chains of the CT protein (CTP) was prepared by SPOT synthesis. The immunoreactivity of membrane-bound peptides with sera from mice vaccinated with an oral inactivated vaccine (Schankol™) allowed the mapping of continuous B-cell epitopes, topological studies, multi-antigen peptide (MAP) synthesis, and Enzyme-Linked Immunosorbent Assay (ELISA) development. Eighteen IgG epitopes were identified; eight in the CTA, three in the CTB, and seven in the protein P. Three V. cholera specific epitopes, Vc/TxA-3, Vc/TxB-11, and Vc/TxP-16, were synthesized as MAP4 and used to coat ELISA plates in order to screen immunized mouse sera. Sensitivities and specificities of 100% were obtained with the MAP4s of Vc/TxA-3 and Vc/TxB-11. The results revealed a set of peptides whose immunoreactivity reflects the immune response to vaccination. The array of peptide data can be applied to develop improved serological tests in order to detect cholera toxin exposure, as well as next generation vaccines to induce more specific antibodies against the cholera toxin. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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12 pages, 2916 KiB

Open AccessArticle

Evaluation of the Combined Effect of Artemisinin and Ferroptosis Inducer RSL3 against Toxoplasma gondii

by Mao Huang, Xinru Cao, Yucong Jiang, Yuehong Shi, Yazhen Ma, Dandan Hu and Xingju Song

Int. J. Mol. Sci. 2023, 24(1), 229; https://doi.org/10.3390/ijms24010229 - 23 Dec 2022

Cited by 3 | Viewed by 1938

Abstract

Toxoplasma gondii is a widespread intracellular pathogen that infects humans and a variety of animals. Dihydroartemisinin (DHA), an effective anti-malarial drug, has potential anti-T. gondii activity that induces ferroptosis in tumor cells, but the mechanism by which it kills T. gondii is not fully understood. In this study, the mechanism of DHA inhibiting T. gondii growth and its possible drug combinations are described. DHA potently inhibited T. gondii with a half-maximal effective concentration (EC₅₀) of 0.22 μM. DHA significantly increased the ROS level of parasites and decreased the mitochondrial membrane potential, which could be reversed by ferroptosis inhibitors (DFO). Moreover, the ferroptosis inducer RSL3 inhibited T. gondii with an EC₅₀ of 0.75 μM. In addition, RSL3 enhanced the DHA-induced ROS level, and the combination of DHA and RSL3 significantly increased the anti-Toxoplasma effect as compared to DHA alone. In summary, we found that DHA-induced ROS accumulation in tachyzoites may be an important cause of T. gondii growth inhibition. Furthermore, we found that the combination of DHA and RSL3 may be an alternative to toxoplasmosis. These results will provide a new strategy for anti-Toxoplasma drug screening and clinical medication guidance. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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16 pages, 4206 KiB

Open AccessArticle

Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket

by Valdir Ferreira de Paula Junior, Mauricio Fraga van Tilburg, Pablo Abreu Morais, Francisco Franciné Maia Júnior, Elza Gadelha Lima, Victor Tabosa dos Santos Oliveira, Maria Izabel Florindo Guedes, Ewerton Wagner Santos Caetano and Valder Nogueira Freire

Int. J. Mol. Sci. 2022, 23(17), 10088; https://doi.org/10.3390/ijms231710088 - 03 Sep 2022

Cited by 3 | Viewed by 1364

Abstract

The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this paper, we evaluated the co-crystallized structures of the protease with the inhibitors benzoic acid (5YOD) and benzimidazole-1-ylmethanol (5H4I). We applied a protocol consisting of two steps: first, classical molecular mechanics energy minimization followed by classical molecular dynamics were performed, obtaining stabilized molecular geometries; second, the optimized/relaxed geometries were used in quantum biochemistry and molecular mechanics/Poisson–Boltzmann surface area (MM-PBSA) calculations to estimate the ligand interactions with each amino acid residue of the binding pocket. We show that the quantum-level results identified essential residues for the stabilization of the 5YOD and 5H4I complexes after classical energy minimization, matching previously published experimental data. The same success, however, was not observed for the MM-PBSA simulations. The application of quantum biochemistry methods seems to be more promising for the design of novel inhibitors acting on NS2B-NS3. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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9 pages, 1780 KiB

Open AccessCommunication

Epipharyngeal Abrasive Therapy (EAT) Reduces the mRNA Expression of Major Proinflammatory Cytokine IL-6 in Chronic Epipharyngitis

by Kensuke Nishi, Shohei Yoshimoto, Soichiro Nishi, Tatsuro Nishi, Ryushiro Nishi, Takayuki Tanaka, Toshiyuki Tsunoda, Kazuaki Imai, Hiroaki Tanaka, Osamu Hotta, Ayaki Tanaka, Kenji Hiromatsu, Senji Shirasawa, Takashi Nakagawa and Takafumi Yamano

Int. J. Mol. Sci. 2022, 23(16), 9205; https://doi.org/10.3390/ijms23169205 - 16 Aug 2022

Cited by 8 | Viewed by 7686

Abstract

The epipharynx, located behind the nasal cavity, is responsible for upper respiratory tract immunity; however, it is also the site of frequent acute and chronic inflammation. Previous reports have suggested that chronic epipharyngitis is involved not only in local symptoms such as cough and postnasal drip, but also in systemic inflammatory diseases such as IgA nephropathy and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and Long COVID. Epipharyngeal Abrasive Therapy (EAT), which is an effective treatment for chronic epipharyngitis in Japan, is reported to be effective for these intractable diseases. The sedation of chronic epipharyngitis by EAT induces suppression of the inflammatory cytokines and improves systemic symptoms, which is considered to be one of the mechanisms, but there is no report that has proved this hypothesis. The purpose of this study was to clarify the anti-inflammatory effect of EAT histologically. The study subjects were 8 patients who were not treated with EAT and 11 patients who were treated with EAT for chronic epipharyngitis for 1 month or more. For immunohistochemical assessment, the expression pattern of IL-6 mRNA, which plays a central role in the human cytokine network, was analyzed using in situ hybridization. The expression of IL-6 in the EAT-treated group was significantly lower than those in the EAT nontreated group (p = 0.0015). In addition, EAT suppressed the expression of tumor necrosis factor alpha (TNFα), a crucial proinflammatory cytokine. As a result, continuous EAT suppressed submucosal cell aggregation and reduced inflammatory cytokines. Thus, EAT may contribute to the improvement of systemic inflammatory diseases through the suppression of IL-6 expression. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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Review

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11 pages, 1116 KiB

Open AccessReview

How Do Anti-SARS-CoV-2 mRNA Vaccines Protect from Severe Disease?

by Maurizio Federico

Int. J. Mol. Sci. 2022, 23(18), 10374; https://doi.org/10.3390/ijms231810374 - 08 Sep 2022

Cited by 8 | Viewed by 2489

Abstract

COVID-19 pathogenesis develops in two phases. First, Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 spreads within the epithelial cells of the mucosa of upper and, possibly, lower respiratory tracts. While the virus dissemination can be controlled by an emerging adaptive host immune response, if the virus diffuses to the pulmonary alveoli, a potentially lethal mechanism can arise in the second phase. It consists of an uncontrolled burst of cytokines/inflammatory factors (i.e., cytokine storm), leading to the insurgence of respiratory symptoms and, consequently, multi-organ failures. Messenger (m)RNA-based vaccines represent the most innovative approach in terms of prophylaxis against SARS-CoV-2-induced disease. The cumulating data indicate that the response to mRNA vaccines is basically ineffective to counteract the viral replication in the upper respiratory tracts, while showing efficacy in containing the development of severe disease. Considering that the antiviral immunity elicited by intramuscularly delivered mRNA vaccines is expected to show similar quantitative and qualitative features in upper and lower respiratory tracts, the different outcomes appear surprising and deserve accurate consideration. In this review, a still unexplored mechanism accounting for the mRNA vaccine effect against severe disease is proposed. Based on well-established experimental evidence, a possible inhibitory effect on alveolar macrophages as a consequence of the diffusion of the extracellular and/or cell-associated Spike protein can be envisioned as a key event counteracting the cytokine storm. This benefit, however, may be associated with defects in the immune functions of macrophages in other tissues whose possible consequences deserve careful evaluation. Full article

(This article belongs to the Special Issue Recent Advances of Biochemistry and Molecular Biology of Infectious Diseases)

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