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Ahlawat S, Shukla BN, Singh V, Sharma Y, Choudhary P, Rao A. GLYCOCINS: The sugar peppered antimicrobials. Biotechnol Adv 2024; 75:108415. [PMID: 39033836 DOI: 10.1016/j.biotechadv.2024.108415] [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: 12/13/2023] [Revised: 06/19/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Glycosylated bacteriocins, known as glycocins, were first discovered in 2011. These bioactive peptides are produced by bacteria to gain survival advantages. They exhibit diverse types of glycans and demonstrate varied antimicrobial activity. Currently, there are 13 experimentally known glycocins, with over 250 identified in silico across different bacterial phyla. Notably, glycocins are recognized for their glycan-mediated antimicrobial activity, proving effective against drug-resistant and foodborne pathogens. Many glycocins contain rare S-linked glycans. Glycosyltransferases (GTs), responsible for transferring sugar to glycocins and involved in glycocin biosynthesis, often cluster together in the producer's genome. This clustering makes them valuable for custom glycoengineering with diverse substrate specificities. Heterologous expression of glycocins has paved the way for the establishment of microbial factories for glycopeptide and glycoconjugate production across various industries. In this review, we emphasize the primary roles of fully and partially characterized glycocins and their glycosylating enzymes. Additionally, we explore how specific glycan structures facilitate these functions in antibacterial activities. Furthermore, we discuss newer approaches and increasing efforts aimed at exploiting bacterial glycobiology for the development of food preservatives and as replacements or complements to traditional antibiotics, particularly in the face of antibiotic-resistant pathogenic bacteria.
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Affiliation(s)
- Shimona Ahlawat
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India
| | | | - Vaidhvi Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Yogita Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | | | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India; Academy of Scientific and Innovation Research (AcSIR), Ghaziabad 201002, India; Current address: Food Safety and Standards Authority of India (FSSAI), New Delhi 110002, India.
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2
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Chen JY, Huang TR, Hsu SY, Huang CC, Wang HS, Chang JS. Effect and mechanism of quercetin or quercetin-containing formulas against COVID-19: From bench to bedside. Phytother Res 2024; 38:2597-2618. [PMID: 38479376 DOI: 10.1002/ptr.8175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 06/13/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the global coronavirus disease 2019 (COVID-19) pandemic since 2019. Immunopathogenesis and thromboembolic events are central to its pathogenesis. Quercetin exhibits several beneficial activities against COVID-19, including antiviral, anti-inflammatory, immunomodulatory, antioxidative, and antithrombotic effects. Although several reviews have been published, these reviews are incomplete from the viewpoint of translational medicine. The authors comprehensively evaluated the evidence of quercetin against COVID-19, both basically and clinically, to apply quercetin and/or its derivatives in the future. The authors searched the PubMed, Embase, and the Cochrane Library databases without any restrictions. The search terms included COVID-19, SARS-CoV-2, quercetin, antiviral, anti-inflammatory, immunomodulatory, thrombosis, embolism, oxidative, and microbiota. The references of relevant articles were also reviewed. All authors independently screened and reviewed the quality of each included manuscript. The Cochrane Risk of Bias Tool, version 2 (RoB 2) was used to assess the quality of the included randomized controlled trials (RCTs). All selected studies were discussed monthly. The effectiveness of quercetin against COVID-19 is not solid due to methodological flaws in the clinical trials. High-quality studies are also required for quercetin-containing traditional Chinese medicines. The low bioavailability and highly variable pharmacokinetics of quercetin hinder its clinical applications. Its positive impact on immunomodulation through reverting dysbiosis of gut microbiota still lacks robust evidence. Quercetin against COVID-19 does not have tough clinical evidence. Strategies to improve its bioavailability and/or to develop its effective derivatives are needed. Well-designed RCTs are also crucial to confirm their effectiveness in the future.
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Affiliation(s)
- Jhong Yuan Chen
- Department of Traditional Chinese Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tsung Rung Huang
- Department of Traditional Chinese Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shih Yun Hsu
- Department of Traditional Chinese Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching Chun Huang
- Department of Traditional Chinese Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Huei Syun Wang
- Department of Traditional Chinese Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jung San Chang
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- PhD Program in Toxicology, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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3
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Chen K, Yang J, Guo X, Han W, Wang H, Zeng X, Wang Z, Yuan Y, Yue T. Microflora structure and functional capacity in Tibetan kefir grains and selenium-enriched Tibetan kefir grains: A metagenomic analysis. Food Microbiol 2024; 119:104454. [PMID: 38225054 DOI: 10.1016/j.fm.2023.104454] [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: 10/02/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 01/17/2024]
Abstract
Tibetan kefir grains (TKGs) are a complex protein-lipid-polysaccharide matrix composed of various microorganisms. Microorganisms have the benefit of being effective, secure, and controllable when used for selenium enrichment. In this study, selenium-enriched Tibetan kefir grains (Se-TKGs) were made, and the microbiology composition was analyzed through a metagenomic analysis, to explore the influence of selenium enrichment. The microbial composition of TKGs and Se-TKGs, as well as the probiotic species, quorum sensing system (QS) and functional genes were compared and evaluated. Lactobacillus kefiranofaciens was the most abundant microbial species in both communities. Compared with TKGs, Se-TKGs had a much higher relative abundance of acetic acid bacteria. Lactobacillus helveticus was the most common probiotic species both in TKGs and Se-TKGs. Probiotics with antibacterial and anti-inflammatory properties were more abundant in Se-TKGs. QS analysis revealed that Se-TKGs contained more QS system-associated genes than TKGs. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that the pathway for human disease ko01501 had the greatest relative abundance in both TKGs and Se-TKGs. Compared with TKGs, Se-TKGs demonstrated a greater relative abundance of different drug resistance-related metabolic pathways. Additionally, linear discriminant analysis effect size was used to examine the biomarkers responsible for the difference between the two groups. In this study, we focused on the microbiological structure of TKGs and Se-TKGs, with the aim of establishing a foundation for a more thorough investigation of Se-TKGs and providing a basis for exploring potential future use.
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Affiliation(s)
- Ke Chen
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; College of Food Science and Technology, Northwest University, Xi'an, 710069, China.
| | - Jinyi Yang
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China.
| | - Xinyuan Guo
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China.
| | - Weiyu Han
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China.
| | - Huijuan Wang
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China.
| | - Xuejun Zeng
- College of Food Science and Technology, Northwest University, Xi'an, 710069, China.
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China.
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; College of Food Science and Technology, Northwest University, Xi'an, 710069, China.
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A & F University, Yangling, 712100, China; College of Food Science and Technology, Northwest University, Xi'an, 710069, China.
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4
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Taufer CR, da Silva J, Rampelotto PH. The Influence of Probiotic Lactobacilli on COVID-19 and the Microbiota. Nutrients 2024; 16:1350. [PMID: 38732597 PMCID: PMC11085918 DOI: 10.3390/nu16091350] [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: 03/07/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024] Open
Abstract
This comprehensive review explores the potential of using lactobacilli as a probiotic in the management of COVID-19. Our findings suggest that lactobacilli show promise in reducing the risk of death, gastrointestinal and overall symptoms, and respiratory failure, as well as in lowering cytokines and inflammatory markers associated with the disease. The molecular mechanisms by which lactobacilli protect against COVID-19 and other viral infections may be related to the reduction in inflammation, modulation of the immune response, and direct interaction with viruses to produce antiviral substances. However, the selected studies demonstrate the presence of mixed findings for various clinical, biochemical, hematological, and immunological parameters, which may be attributed to methodological differences among studies. We highlight the importance of clearly describing randomization processes to minimize bias and caution against small sample sizes and inappropriate statistical tests that could lead to errors. This review offers valuable insights into the therapeutic potential of lactobacilli in the context of COVID-19 and identifies avenues for further research and applications. These findings hold promise for the development of novel approaches to managing COVID-19 and warrant further investigation into the potential benefits of lactobacilli in combating the disease.
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Affiliation(s)
- Clarissa Reginato Taufer
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Juliana da Silva
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
- Graduate Program in Health and Human Development, Universidade La Salle, Canoas 92010-000, Brazil
| | - Pabulo Henrique Rampelotto
- Bioinformatics and Biostatistics Core Facility, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
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Giovanetti M, Pannella G, Altomare A, Rocchi G, Guarino M, Ciccozzi M, Riva E, Gherardi G. Exploring the Interplay between COVID-19 and Gut Health: The Potential Role of Prebiotics and Probiotics in Immune Support. Viruses 2024; 16:370. [PMID: 38543736 PMCID: PMC10975078 DOI: 10.3390/v16030370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 05/23/2024] Open
Abstract
The COVID-19 pandemic has profoundly impacted global health, leading to extensive research focused on developing strategies to enhance outbreak response and mitigate the disease's severity. In the aftermath of the pandemic, attention has shifted towards understanding and addressing long-term health implications, particularly in individuals experiencing persistent symptoms, known as long COVID. Research into potential interventions to alleviate long COVID symptoms has intensified, with a focus on strategies to support immune function and mitigate inflammation. One area of interest is the gut microbiota, which plays a crucial role in regulating immune responses and maintaining overall health. Prebiotics and probiotics, known for their ability to modulate the gut microbiota, have emerged as potential therapeutic agents in bolstering immune function and reducing inflammation. This review delves into the intricate relationship between long COVID, the gut microbiota, and immune function, with a specific focus on the role of prebiotics and probiotics. We examine the immune response to long COVID, emphasizing the importance of inflammation and immune regulation in the persistence of symptoms. The potential of probiotics in modulating immune responses, including their mechanisms in combating viral infections such as COVID-19, is discussed in detail. Clinical evidence supporting the use of probiotics in managing long COVID symptoms is summarized, highlighting their role as adjunctive therapy in addressing various aspects of SARS-CoV-2 infection and its aftermath.
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Affiliation(s)
- Marta Giovanetti
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Roma, Italy; (G.P.); (A.A.)
- Climate Amplified Diseases and Epidemics (CLIMADE), Brasilia 70070-130, Brazil
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-002, Brazil
| | - Gianfranco Pannella
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Roma, Italy; (G.P.); (A.A.)
- Department of Agricultural, Enviromental and Food Science, University of Molise, 86100 Campobasso, Italy
| | - Annamaria Altomare
- Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Roma, Italy; (G.P.); (A.A.)
- Research Unit of Gastroenterology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (G.R.); (M.G.)
| | - Giulia Rocchi
- Research Unit of Gastroenterology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (G.R.); (M.G.)
| | - Michele Guarino
- Research Unit of Gastroenterology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (G.R.); (M.G.)
- Operative Research Unit of Gastroenterology, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Roma, Italy;
| | - Elisabetta Riva
- Unit of Virology, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, Italy;
- Applied Bacteriological Sciences Unit, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Giovanni Gherardi
- Applied Bacteriological Sciences Unit, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
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Taufer CR, Rampelotto PH. Lactobacilli in COVID-19: A Systematic Review Based on Next-Generation Sequencing Studies. Microorganisms 2024; 12:284. [PMID: 38399688 PMCID: PMC10891515 DOI: 10.3390/microorganisms12020284] [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: 12/28/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The global pandemic was caused by the SARS-CoV-2 virus, known as COVID-19, which primarily affects the respiratory and intestinal systems and impacts the microbial communities of patients. This systematic review involved a comprehensive search across the major literature databases to explore the relationship between lactobacilli and COVID-19. Our emphasis was on investigations employing NGS technologies to explore this connection. Our analysis of nine selected studies revealed that lactobacilli have a reduced abundance in the disease and an association with disease severity. The protective mechanisms of lactobacilli in COVID-19 and other viral infections are likely to be multifaceted, involving complex interactions between the microbiota, the host immune system, and the virus itself. Moreover, upon closely examining the NGS methodologies and associated statistical analyses in each research study, we have noted concerns regarding the approach used to delineate the varying abundance of lactobacilli, which involves potential biases and the exclusion of pertinent data elements. These findings provide new insight into the relationship between COVID-19 and lactobacilli, highlighting the potential for microbiota modulation in COVID-19 treatment.
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Affiliation(s)
- Clarissa Reginato Taufer
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Pabulo Henrique Rampelotto
- Bioinformatics and Biostatistics Core Facility, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
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Abedi Dorcheh F, Balmeh N, Hejazi SH, Allahyari Fard N. Investigation of the mutated antimicrobial peptides to inhibit ACE2, TMPRSS2 and GRP78 receptors of SARS-CoV-2 and angiotensin II type 1 receptor (AT1R) as well as controlling COVID-19 disease. J Biomol Struct Dyn 2023:1-24. [PMID: 38109185 DOI: 10.1080/07391102.2023.2292307] [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: 12/08/2022] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
SARS-CoV-2 is a global problem nowadays. Based on studies, some human receptors are involved in binding to SARS-CoV-2. Thus, the inhibition of these receptors can be effective in the treatment of Covid-19. Because of the proven benefits of antimicrobial peptides (AMPs) and the side effects of chemical drugs, they can be known as an alternative to recent medicines. RCSB PDB to obtain PDB id, StraPep and PhytAMP to acquire Bio-AMPs information and 3-D structure, and AlgPred, Toxinpred, TargetAntiAngio, IL-4pred, IL-6pred, ACPred and Hemopred databases were used to find the best score peptide features. HADDOCK 2.2 was used for molecular docking analysis, and UCSF Chimera software version 1.15, SWISS-MODEL and BIOVIA Discovery Studio Visualizer4.5 were used for mutation and structure modeling. Furthermore, MD simulation results were achieved from GROMACS 4.6.5. Based on the obtained results, the Moricin peptide was found to have the best affinity for ACE2. Moreover, Bacteriocin leucocin-A had the highest affinity for GRP78, Cathelicidin-6 had the best affinity for AT1R, and Bacteriocin PlnK had the best binding affinity for TMPRSS2. Additionally, Bacteriocin glycocin F, Bacteriocin lactococcin-G subunit beta and Cathelicidin-6 peptides were the most common compounds among the four receptors. However, these peptides also have some side effects. Consequently, the mutation eliminated the side effects, and MD simulation results indicated that the mutation proved the result of the docking analysis. The effect of AMPs on ACE2, GRP78, TMPRSS2 and AT1R receptors can be a novel treatment for Covid-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatemeh Abedi Dorcheh
- Department of Biotechnology, School of Bioscience and Biotechnology, Shahid Ashrafi Esfahani University of Isfahan, Sepahan Shahr, Iran
| | - Negar Balmeh
- Skin Diseases and Leishmaniasis Research Center, Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Hossein Hejazi
- Skin Diseases and Leishmaniasis Research Center, Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Najaf Allahyari Fard
- Department of Systems Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, Iran
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8
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Erol I, Kotil SE, Ortakci F, Durdagi S. Exploring the binding capacity of lactic acid bacteria derived bacteriocins against RBD of SARS-CoV-2 Omicron variant by molecular simulations. J Biomol Struct Dyn 2023; 41:10774-10784. [PMID: 36591650 DOI: 10.1080/07391102.2022.2158934] [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: 07/22/2022] [Accepted: 12/10/2022] [Indexed: 01/03/2023]
Abstract
The changes in the SARS-CoV-2 genome have resulted in the emergence of new variants. Some of the variants have been classified as variants of concern (VOC). These strains have higher transmission rate and improved fitness. One of the prevalent were the Omicron variant. Unlike previous VOCs, the Omicron possesses fifteen mutations on the spike protein's receptor binding domain (RBD). The modifications of spike protein's key amino acid residues facilitate the virus' binding capability against ACE2, resulting in an increase in the infectiousness of Omicron variant. Consequently, investigating the prevention and treatment of the Omicron variant is crucial. In the present study, we aim to explore the binding capacity of twenty-two bacteriocins derived from Lactic Acid Bacteria (LAB) against the Omicron variant by using protein-peptidedocking and molecular dynamics (MD) simulations. The Omicron variant RBD was prepared by introducing fifteen mutations using PyMol. The protein-peptide complexes were obtained using HADDOCK v2.4 docking webserver. Top scoring complexes obtained from HADDOCK webserver were retrieved and submitted to the PRODIGY server for the prediction of binding energies. RBD-bacteriocin complexes were subjected to MD simulations. We discovered promising peptide-based therapeutic candidates for the inhibition of Omicron variant for example Salivaricin B, Pediocin PA 1, Plantaricin W, Lactococcin mmfii and Enterocin A. The lead bacteriocins, except Enterocin A, are biosynthesized by food-grade lactic acid bacteria. Our study puts forth a preliminary information regarding potential utilization of food-grade LAB-derived bacteriocins, particularly Salivaricin B and Pediocin PA 1, for Covid-19 treatment and prophylaxis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Seyfullah Enes Kotil
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Fatih Ortakci
- Bioengineering Department, Faculty of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
- School of Pharmacy, Bahcesehir University, Istanbul, Turkey
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9
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Prasad R, Ajith H, Kumar Chandrakumaran N, Dnyaneshwar Khangar P, Mohan A, Nelson-Sathi S. In silico study identifies peptide inhibitors that negate the effect of non-synonymous mutations in major drug targets of SARS-CoV-2 variants. J Biomol Struct Dyn 2023; 41:9551-9561. [PMID: 36377464 DOI: 10.1080/07391102.2022.2143426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2022]
Abstract
Since its advent in December 2019, SARS-CoV-2 has diverged into multiple variants with differing levels of virulence owing to the accumulation of mutations in its genome. The structural changes induced by non-synonymous mutations in major drug targets of the virus are known to alter the binding of potential antagonistic inhibitors. Here, we analyzed the effects of non-synonymous mutations in major targets of SARS-CoV-2 in response to potential peptide inhibitors. We screened 12 peptides reported to have anti-viral properties against RBD and 5 peptides against Mpro of SARS-CoV-2 variants using molecular docking and simulation approaches. The mutational landscape of RBD among SARS-CoV-2 variants had 21 non-synonymous mutations across 18 distinct sites. Among these, 14 mutations were present in the RBM region directly interacting with the hACE2 receptor. However, Only 3 non-synonymous mutations were observed in Mpro. We found that LCB1 - a de novo-synthesized peptide has the highest binding affinity to RBD despite non-synonymous mutations in variants and engages key residues of RBD-hACE2 interaction such as K417, E484, N487, and N501. Similarly, an antimicrobial peptide; 2JOS, was identified against Mpro with high binding affinity as it interacts with key residues in dimerization sites such as E166 and F140 crucial for viral replication. MD simulations affirm the stability of RBD-LCB1 and Mpro-2JOS complexes with an average RMSD of 1.902 and 2.476 respectively. We ascertain that LCB1 and 2JOS peptides are promising inhibitors to combat emerging variants of SARS-CoV-2 and thus warrant further investigations using in-vitro and in-vivo analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshny Prasad
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Harikrishnan Ajith
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | | | - Anand Mohan
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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10
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Antony MA, Patel S, Verma V, Kant R. The Role of Gut Microbiome Supplementation in COVID-19 Management. Cureus 2023; 15:e46960. [PMID: 38021562 PMCID: PMC10640765 DOI: 10.7759/cureus.46960] [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] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
COVID-19, which is caused by the RNA virus, SARS-CoV-2, mainly affects the respiratory system and has a varied clinical presentation. However, several studies have shown that COVID-19 can also affect the gastrointestinal (GI) system. Patients can experience various GI symptoms, such as vomiting and diarrhea, and the virus has been detected in the stool samples of patients hospitalized with COVID-19. There have also been rare reports of COVID-19 presenting with isolated GI symptoms and lack of respiratory symptoms, and the virus has also been detected for prolonged periods in the fecal samples of COVID-19 patients. Major alterations in the gut microbiome in the form of depletion of beneficial organisms and an abundance of pathogenic organisms have been reported in the fecal samples of hospitalized COVID-19 patients. Although the US FDA has approved several drugs to manage COVID-19, their efficacy remains modest. So, there is a constant ongoing effort to investigate novel treatment options for COVID-19. Health supplements like probiotics, prebiotics, postbiotics, and synbiotics have been popularly known for their various health benefits. In this review, we have summarized the current literature, which shows the potential benefit of these health supplements to mitigate and/or prevent the clinical presentation of COVID-19.
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Affiliation(s)
- Mc Anto Antony
- Department of Endocrinology, Diabetes and Metabolism, Medical University of South Carolina, Anderson, USA
| | - Siddharth Patel
- Department of Internal Medicine, Decatur Morgan Hospital, Decatur, USA
| | - Vipin Verma
- Department of Internal Medicine, Medical University of South Carolina, Anderson, USA
| | - Ravi Kant
- Department of Endocrinology, Diabetes and Metabolism, Medical University of South Carolina, Anderson, USA
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11
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Barman P, Joshi S, Sharma S, Preet S, Sharma S, Saini A. Strategic Approaches to Improvise Peptide Drugs as Next Generation Therapeutics. Int J Pept Res Ther 2023; 29:61. [PMID: 37251528 PMCID: PMC10206374 DOI: 10.1007/s10989-023-10524-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 05/31/2023]
Abstract
In recent years, the occurrence of a wide variety of drug-resistant diseases has led to an increase in interest in alternate therapies. Peptide-based drugs as an alternate therapy hold researchers' attention in various therapeutic fields such as neurology, dermatology, oncology, metabolic diseases, etc. Previously, they had been overlooked by pharmaceutical companies due to certain limitations such as proteolytic degradation, poor membrane permeability, low oral bioavailability, shorter half-life, and poor target specificity. Over the last two decades, these limitations have been countered by introducing various modification strategies such as backbone and side-chain modifications, amino acid substitution, etc. which improve their functionality. This has led to a substantial interest of researchers and pharmaceutical companies, moving the next generation of these therapeutics from fundamental research to the market. Various chemical and computational approaches are aiding the production of more stable and long-lasting peptides guiding the formulation of novel and advanced therapeutic agents. However, there is not a single article that talks about various peptide design approaches i.e., in-silico and in-vitro along with their applications and strategies to improve their efficacy. In this review, we try to bring different aspects of peptide-based therapeutics under one article with a clear focus to cover the missing links in the literature. This review draws emphasis on various in-silico approaches and modification-based peptide design strategies. It also highlights the recent progress made in peptide delivery methods important for their enhanced clinical efficacy. The article would provide a bird's-eye view to researchers aiming to develop peptides with therapeutic applications. Graphical Abstract
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Affiliation(s)
- Panchali Barman
- Institute of Forensic Science and Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014 India
| | - Shubhi Joshi
- Energy Research Centre, Panjab University, Sector 14, Chandigarh, 160014 India
| | - Sheetal Sharma
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
| | - Simran Preet
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
| | - Shweta Sharma
- Institute of Forensic Science and Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014 India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
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12
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Nanomedicine for drug resistant pathogens and COVID-19 using mushroom nanocomposite inspired with bacteriocin – A Review. INORG CHEM COMMUN 2023; 152:110682. [PMID: 37041990 PMCID: PMC10067464 DOI: 10.1016/j.inoche.2023.110682] [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: 03/25/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
Multidrug resistant (MDR) pathogens have become a major global health challenge and have severely threatened the health of society. Current conditions have gotten worse as a result of the COVID-19 pandemic, and infection rates in the future will rise. It is necessary to design, respond effectively, and take action to address these challenges by investigating new avenues. In this regard, the fabrication of metal NPs utilized by various methods, including green synthesis using mushroom, is highly versatile, cost-effective, eco-compatible, and superior. In contrast, biofabrication of metal NPs can be employed as a powerful weapon against MDR pathogens and have immense biomedical applications. In addition, the advancement in nanotechnology has made possible to modify the nanomaterials and enhance their activities. Metal NPs with biomolecules composite to prevents their microbial adhesion and kills the microbial pathogens through biofilm formation. Bacteriocin is an excellent antimicrobial peptide that works well as an augmentation substance to boost the antimicrobial effects. As a result, we concentrate on the creation of new, eco-compatible mycosynthesized metal NPs with bacteriocin nanocomposite via electrostatic, covalent, or non-covalent bindings. The synergistic benefits of metal NPs with bacteriocin to combat MDR pathogens and COVID-19, as well as other biomedical applications, are discussed in this review. Moreover, the importance of the adverse outcome pathway (AOP) in risk analysis of manufactured metal nanocomposite nanomaterial and their future possibilities also discussed.
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13
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Valdebenito-Navarrete H, Fuentes-Barrera V, Smith CT, Salas-Burgos A, Zuniga FA, Gomez LA, García-Cancino A. Can Probiotics, Particularly Limosilactobacillus fermentum UCO-979C and Lacticaseibacillus rhamnosus UCO-25A, Be Preventive Alternatives against SARS-CoV-2? BIOLOGY 2023; 12:biology12030384. [PMID: 36979076 PMCID: PMC10045641 DOI: 10.3390/biology12030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/07/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023]
Abstract
COVID-19, an infection produced by the SARS-CoV-2 virus in humans, has rapidly spread to become a high-mortality pandemic. SARS-CoV-2 is a single-stranded RNA virus characterized by infecting epithelial cells of the intestine and lungs, binding to the ACE2 receptor present on epithelial cells. COVID-19 treatment is based on antivirals and antibiotics against symptomatology in addition to a successful preventive strategy based on vaccination. At this point, several variants of the virus have emerged, altering the effectiveness of treatments and thereby attracting attention to several alternative therapies, including immunobiotics, to cope with the problem. This review, based on articles, patents, and an in silico analysis, aims to address our present knowledge of the COVID-19 disease, its symptomatology, and the possible beneficial effects for patients if probiotics with the characteristics of immunobiotics are used to confront this disease. Moreover, two probiotic strains, L. fermentum UCO-979C and L. rhamnosus UCO-25A, with different effects demonstrated at our laboratory, are emphasized. The point of view of this review highlights the possible benefits of probiotics, particularly those associated with immunomodulation as well as the production of secondary metabolites, and their potential targets during SARS-CoV-2 infection.
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Affiliation(s)
- Héctor Valdebenito-Navarrete
- Laboratory of Bacterial Pathogenicity, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción 4070386, Chile
| | - Victor Fuentes-Barrera
- Laboratory of Bacterial Pathogenicity, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción 4070386, Chile
| | - Carlos T. Smith
- Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción 4070386, Chile
| | - Alexis Salas-Burgos
- Department of Pharmacology, Faculty of Biological Sciences, Universidad de Concepción, Concepción 4070386, Chile
| | - Felipe A. Zuniga
- Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, Universidad de Concepción, Víctor Lamas 1290, Concepción 4030000, Chile
| | - Leonardo A. Gomez
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción 4070386, Chile
| | - Apolinaria García-Cancino
- Laboratory of Bacterial Pathogenicity, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción 4070386, Chile
- Correspondence: ; Tel.: +56-41-2204144; Fax: +56-41-2245975
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14
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Chakrobarty S, Garai S, Ghosh A, Mukerjee N, Das D. Bioactive plantaricins as potent anti-cancer drug candidates: double docking, molecular dynamics simulation and in vitro cytotoxicity analysis. J Biomol Struct Dyn 2023; 41:13605-13615. [PMID: 36775653 DOI: 10.1080/07391102.2023.2177732] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/02/2023] [Indexed: 02/14/2023]
Abstract
The medical community is desperate for a reliable source of medications to alleviate the severity of conventional cancer treatments and prevent secondary microbial infections in oncological patients. In this regard, plantaricins from lactic acid bacteria were explored as prospective drug candidates against known anti-cancer drug targets. Three plantaricins, JLA-9, GZ1-27 and BN, have a binding affinity of -8.8, -8.6 and -7.2 kcal/mol, respectively, with squalene synthase (SQS), a key molecule in lung cancer metastasis. All three plantaricins displayed analogous binding patterns as SQS inhibitors and generated hydrogen and hydrophobic interactions with ARG 47, ARG 188, PHE24, LEU183 and PRO292. Structural stability of docked complexes was validated using molecular dynamics simulation derived parameters such as RMSD, RMSF and radius of gyration. Based on MD simulation results, conformational changes and stabilities of docked SQS/plantaricin complexes with respect to the time frame were evaluated using machine learning (logistic regression algorithm). Double docking with SQS/matrix metalloproteinase MMP1 and PCA analysis revealed the potential of plantaricin JLA-9 as a multi-substrate inhibitor. Further, plantaricin JLA-9 induced a significant cytotoxic response against the lung carcinoma cell line (A549) in a dose and time dependent manner with inhibition concentration (IC50) of 0.082 µg/ml after 48 h. However, plantaricin JLA-9 did not induce cytotoxicity in normal lung cells (L-132), as the IC50 value was not obtained even at a higher dose of 0.8 µg/ml. In silico pharmacokinetic (ADMET) profile implies that plantaricin JLA-9 could be developed as new age anti-cancer therapeutic with a preference for parenteral administration.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Swarnava Garai
- Department of Bioengineering, NIT Agartala, Agartala, India
| | - Arabinda Ghosh
- Department of Botany, Gauhati University, Guwahati, Assam, India
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Barasat, Kolkata, India
| | - Deeplina Das
- Department of Bioengineering, NIT Agartala, Agartala, India
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15
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Mohammadi AH, Behjati M, Karami M, Abari AH, Sobhani-Nasab A, Rourani HA, Hazrati E, Mirghazanfari SM, Hadi V, Hadi S, Milajerdi A. An overview on role of nutrition on COVID-19 immunity: Accumulative review from available studies. CLINICAL NUTRITION OPEN SCIENCE 2023; 47:6-43. [PMID: 36540357 PMCID: PMC9754583 DOI: 10.1016/j.nutos.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
The novel coronavirus infection (COVID-19) conveys a serious global threat to health and economy. A common predisposing factor for development to serious progressive disease is presence of a low-grade inflammation, e.g., as seen in diabetes, metabolic syndrome, and heart failure. Micronutrient deficiencies may also contribute to the development of this state. Therefore, the aim of the present study is to explore the role of the nutrition to relieve progression of COVID-19. According PRISMA protocol, we conducted an online databases search including Scopus, PubMed, Google Scholar and web of science for published literatures in the era of COVID-19 Outbreak regarding to the status of nutrition and COVID-19 until December 2021. There were available studies (80 studies) providing direct evidence regarding the associations between the status of nutrition and COVID-19 infection. Adequate nutritional supply is essential for resistance against other viral infections and also for improvement of immune function and reduction of inflammation. Hence, it is suggested that nutritional intervention which secures an adequate status might protect against the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome - coronavirus-2) and mitigate its course. We also recommend initiation of adequate nutritional supplementation in high-risk areas and/or soon after the time of suspected infection with SARS-CoV-2. Subjects in high-risk groups should have high priority for applying this nutritive adjuvant therapy that should be started prior to administration of specific and supportive medical measures.
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Affiliation(s)
- Amir Hossein Mohammadi
- Department of Biochemistry, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mohaddeseh Behjati
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Masoumeh Karami
- Department of Biochemistry, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Afrouzossadat Hosseini Abari
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
| | - Ali Sobhani-Nasab
- Social Determinants of Health (SDH) Research Center, Kashan University of Medical Sciences, Kashan, Iran
- Core Research Lab, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Amini Rourani
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
| | - Ebrahim Hazrati
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Sayid Mahdi Mirghazanfari
- Department of Physiology and Iranian Medicine, School of Medicine, AJA University of Medical Sciences, Iran
| | - Vahid Hadi
- Department of Health, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Saeid Hadi
- Department of Health, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Alireza Milajerdi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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16
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In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2. Probiotics Antimicrob Proteins 2023; 15:17-29. [PMID: 34837166 PMCID: PMC8626284 DOI: 10.1007/s12602-021-09879-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2021] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its variants. The SARS-CoV-2 virus shows pathogenesis by entering the host cells via spike protein and Angiotensin-Converting Enzyme 2 receptor protein. Thus, the present study aims to compute the binding energies between a wide range of bacteriocins with receptor-binding domain (RBD) on spike proteins of wild type (WT) and beta variant (lineage B.1.351). Molecular docking analyses were performed to evaluate binding energies. Upon achieving the best bio-peptides with the highest docking scores, further molecular dynamics (MD) simulations were performed to validate the structure and interaction stability. Protein-protein docking of the chosen 22 biopeptides with WT-RBD showed docking scores lower than -7.9 kcal/mol. Pediocin PA-1 and salivaricin P showed the lowest (best) docking scores of - 12 kcal/mol. Pediocin PA-1, salivaricin B, and salivaricin P showed a remarkable increase in the double mutant's predicted binding affinity with -13.8 kcal/mol, -13.0 kcal/mol, and -12.5 kcal/mol, respectively. Also, a better predicted binding affinity of pediocin PA-1 and salivaricin B against triple mutant was observed compared to the WT. Thus, pediocin PA-1 binds stronger to mutants of the RBD, particularly to double and triple mutants. Salivaricin B showed a better predicted binding affinity towards triple mutant compared to WT, showing that it might be another bacteriocin with potential activity against the SARS-CoV-2 beta variant. Overall, pediocin PA-1, salivaricin P, and salivaricin B are the most promising candidates for inhibiting SARS-CoV-2 (including lineage B.1.351) entrance into the human cells. These bacteriocins derived from lactic acid bacteria hold promising potential for paving an alternative way for treatment and prophylaxis of WT and beta variants.
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17
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Mabrouk DM. Antimicrobial peptides: features, applications and the potential use against covid-19. Mol Biol Rep 2022; 49:10039-10050. [PMID: 35606604 PMCID: PMC9126628 DOI: 10.1007/s11033-022-07572-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022]
Abstract
BACKGROUND Antimicrobial peptides (AMPs) are a diverse class of molecules that represent a vital part of innate immunity. AMPs are evolutionarily conserved molecules that exhibit structural and functional diversity. They provide a possible solution to the antibiotic-resistance crisis. MAIN TEXT These small cationic peptides can target bacteria, fungi, and viruses, as well as cancer cells. Their unique action mechanisms, rare antibiotic-resistant variants, broad-spectrum activity, low toxicity, and high specificity encourage pharmaceutical industries to conduct clinical trials to develop them as therapeutic drugs. The rapid development of computer-assisted strategies accelerated the identification of AMPs. The Antimicrobial Peptide Database (APD) so far contains 3324 AMPs from different sources. In addition to their applications in different fields, some AMPs demonstrated the potential to combat COVID-19, and hinder viral infectivity in diverse ways. CONCLUSIONS This review provides a brief history of AMPs and their features, including classification, evolution, sources and mechanisms of action, biosynthesis pathway, and identification techniques. Furthermore, their different applications, challenges to clinical applications, and their potential use against COVID-19 are presented.
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Affiliation(s)
- Dalia Mamdouh Mabrouk
- Cell Biology Department, National Research Centre, 33 El Bohouth, St., P.O.12622, Dokki, Giza, Egypt.
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18
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Molecular Docking and In-Silico Analysis of Natural Biomolecules against Dengue, Ebola, Zika, SARS-CoV-2 Variants of Concern and Monkeypox Virus. Int J Mol Sci 2022; 23:ijms231911131. [PMID: 36232431 PMCID: PMC9569982 DOI: 10.3390/ijms231911131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/20/2022] Open
Abstract
The emergence and rapid evolution of human pathogenic viruses, combined with the difficulties in developing effective vaccines, underline the need to develop innovative broad-spectrum antiviral therapeutic agents. The present study aims to determine the in silico antiviral potential of six bacterial antimicrobial peptides (AMPs), two phytochemicals (silvestrol, andrographolide), and two bacterial secondary metabolites (lyngbyabellin A, hapalindole H) against dengue virus, Zika virus, Ebola virus, the major variants of SARS-CoV-2 and monkeypox virus. The comparison of docking scores obtained with natural biomolecules was performed with specific neutralizing antibodies (positive controls for ClusPro) and antiviral drugs (negative controls for Autodock Vina). Glycocin F was the only natural biomolecule tested to show high binding energies to all viral surface proteins and the corresponding viral cell receptors. Lactococcin G and plantaricin ASM1 also achieved high docking scores with all viral surface proteins and most corresponding cell surface receptors. Silvestrol, andrographolide, hapalindole H, and lyngbyabellin A showed variable docking scores depending on the viral surface proteins and cell receptors tested. Three glycocin F mutants with amino acid modifications showed an increase in their docking energy to the spike proteins of SARS-CoV-2 B.1.617.2 Indian variant, and of the SARS-CoV-2 P.1 Japan/Brazil variant, and the dengue DENV envelope protein. All mutant AMPs indicated a frequent occurrence of valine and proline amino acid rotamers. AMPs and glycocin F in particular are the most promising biomolecules for the development of broad-spectrum antiviral treatments targeting the attachment and entry of viruses into their target cell.
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19
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Probiotics in the Management of Mental and Gastrointestinal Post-COVID Symptomes. J Clin Med 2022; 11:jcm11175155. [PMID: 36079082 PMCID: PMC9457065 DOI: 10.3390/jcm11175155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/17/2022] [Accepted: 08/29/2022] [Indexed: 01/30/2023] Open
Abstract
Patients with “post-COVID” syndrome manifest with a variety of signs and symptoms that continue/develop after acute COVID-19. Among the most common are gastrointestinal (GI) and mental symptoms. The reason for symptom occurrence lies in the SARS-CoV-2 capability of binding to exact receptors, among other angiotensin converting enzyme 2 (ACE2) receptors in gastrointestinal lining and neuropilin-1 (NRP-1) in the nervous system, which leads to loss of gastrointestinal and blood-brain barriers integrity and function. The data are mounting that SARS-CoV-2 can trigger systemic inflammation and lead to disruption of gut-brain axis (GBA) and the development of disorders of gut brain interaction (DGBIs). Functional dyspepsia (FD) and irritable bowel syndrome (IBS) are the most common DGBIs syndromes. On the other hand, emotional disorders have also been demonstrated as DGBIs. Currently, there are no official recommendations or recommended procedures for the use of probiotics in patients with COVID-19. However, it can be assumed that many doctors, pharmacists, and patients will want to use a probiotic in the treatment of this disease. In such cases, strains with documented activity should be used. There is a constant need to plan and conduct new trials on the role of probiotics and verify their clinical efficacy for counteracting the negative consequences of COVID-19 pandemic. Quality control is another important but often neglected aspect in trials utilizing probiotics in various clinical entities. It determines the safety and efficacy of probiotics, which is of utmost importance in patients with post-acute COVID-19 syndrome.
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20
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Dahiya D, Nigam PS. Clinical Potential of Microbial Strains, Used in Fermentation for Probiotic Food, Beverages and in Synbiotic Supplements, as Psychobiotics for Cognitive Treatment through Gut-Brain Signaling. Microorganisms 2022; 10:1687. [PMID: 36144289 PMCID: PMC9505539 DOI: 10.3390/microorganisms10091687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 12/14/2022] Open
Abstract
Pure and viable strains of microorganisms identified and characterized as probiotic strains are used in the fermentation process to prepare probiotic food and beverages. These products are sources of nutrition and help in the maintenance of gut microflora. The intake of food products prepared with the use of probiotic microorganisms and containing their metabolites and whole microbial cells can be considered as a natural formulation of synbiotic products with prebiotic substrates and culture. Other than through the intake of fermented food and beverages, probiotic microorganisms can be taken through a supplement, which is a complementary form prepared by combining separate sources of prebiotic substrates and specific probiotic cultures. Whether a fermented solid food or beverage, both the components in the product are in a synergistic relationship and contribute to several health benefits at a lower cost. The aim of this article is to review the relevant literature and present the outcomes of recent studies which have been conducted to explore the clinical potential of probiotic strains and their effect on psychological conditions. Studies have shown the relationship between gut microbiota and the brain, and their interaction through signaling. The studies have concluded that the gut-brain axis can be manipulated with the intake of probiotic foods or synbiotic supplements containing specific probiotic strains accompanied with their complementary prebiotics for the enhanced sustainability of healthy GIT microflora.
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Affiliation(s)
| | - Poonam Singh Nigam
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, UK
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21
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Satwong N, Promsai S. Feasibility Study on Co‐culture
Bacillus coagulans
and
Lacticaseibacillus rhamnosus
Formulated in Probiotic‐supplemented Pigmented Rice Products. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natchaya Satwong
- Division of Microbiology, Department of Science, Faculty of Liberal Arts and Science Kasetsart University Kamphaeng Saen Campus Nakhon Pathom Thailand
| | - Saran Promsai
- Division of Microbiology, Department of Science, Faculty of Liberal Arts and Science Kasetsart University Kamphaeng Saen Campus Nakhon Pathom Thailand
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22
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Khan K, Basharat Z, Jalal K, Mashraqi MM, Alzamami A, Alshamrani S, Uddin R. Identification of Therapeutic Targets in an Emerging Gastrointestinal Pathogen Campylobacter ureolyticus and Possible Intervention through Natural Products. Antibiotics (Basel) 2022; 11:antibiotics11050680. [PMID: 35625323 PMCID: PMC9137744 DOI: 10.3390/antibiotics11050680] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023] Open
Abstract
Campylobacter ureolyticus is a Gram-negative, anaerobic, non-spore-forming bacteria that causes gastrointestinal infections. Being the most prevalent cause of bacterial enteritis globally, infection by this bacterium is linked with significant morbidity and mortality in children and immunocompromised patients. No information on pan-therapeutic drug targets for this species is available yet. In the current study, a pan-genome analysis was performed on 13 strains of C. ureolyticus to prioritize potent drug targets from the identified core genome. In total, 26 druggable proteins were identified using subtractive genomics. To the best of the authors’ knowledge, this is the first report on the mining of drug targets in C. ureolyticus. UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) was selected as a promiscuous pharmacological target for virtual screening of two bacterial-derived natural product libraries, i.e., postbiotics (n = 78) and streptomycin (n = 737) compounds. LpxC inhibitors from the ZINC database (n = 142 compounds) were also studied with reference to LpxC of C. ureolyticus. The top three docked compounds from each library (including ZINC26844580, ZINC13474902, ZINC13474878, Notoginsenoside St-4, Asiaticoside F, Paraherquamide E, Phytoene, Lycopene, and Sparsomycin) were selected based on their binding energies and validated using molecular dynamics simulations. To help identify potential risks associated with the selected compounds, ADMET profiling was also performed and most of the compounds were considered safe. Our findings may serve as baseline information for laboratory studies leading to the discovery of drugs for use against C. ureolyticus infections.
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Affiliation(s)
- Kanwal Khan
- PCMD, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (K.K.); (R.U.)
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan;
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- Correspondence:
| | - Mutaib M. Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (M.M.M.); (S.A.)
| | - Ahmad Alzamami
- Clinical Laboratory Science Department, College of Applied Medical Science, Shaqra University, Al-Quwayiyah 11961, Saudi Arabia;
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (M.M.M.); (S.A.)
| | - Reaz Uddin
- PCMD, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; (K.K.); (R.U.)
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23
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Mahmoudi S, Dehkordi MM, Asgarshamsi MH. The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects. Biophys Chem 2022; 288:106824. [PMID: 35728510 PMCID: PMC9095071 DOI: 10.1016/j.bpc.2022.106824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 05/07/2022] [Indexed: 02/07/2023]
Abstract
The novel coronavirus that caused COVID-19 pandemic is SARS-CoV-2. Although various vaccines are currently being used to prevent the disease's severe consequences, there is still a need for medications for those who become infected. The SARS-CoV-2 has a variety of proteins that have been studied extensively since the virus's advent. In this review article, we looked at chemical to molecular aspects of the various structures studied that have pharmaceutical activity and attempted to find a link between drug activity and compound structure. For example, designing of the compounds which bind to the allosteric site and modify hydrogen bonds or the salt bridges can disrupt SARS-CoV2 RBD–ACE2 complex. It seems that quaternary ammonium moiety and quinolin-1-ium structure could act as a negative allosteric modulator to reduce the tendency between spike-ACE2. Pharmaceutical structures with amino heads and hydrophobic tails can block envelope protein to prevent making mature SARS-CoV-2. Also, structures based on naphthalene pharmacophores or isosteres can form a strong bond with the PLpro and form a π-π and the Mpro's active site can be occupied by octapeptide compounds or linear compounds with a similar fitting ability to octapeptide compounds. And for protein RdRp, it is critical to consider pH and pKa so that pKa regulation of compounds to comply with patients is very effective, thus, the presence of tetrazole, phenylpyrazole groups, and analogs of pyrophosphate in the designed drugs increase the likelihood of the RdRp active site inhibition. Finally, it can be deduced that designing hybrid drug molecules along with considering the aforementioned characteristics would be a suitable approach for developing medicines in order to accurate targeting and complete inhibition this virus.
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Affiliation(s)
- Samira Mahmoudi
- Department of Microbial Biotechnology, School of Biological Sciences, Islamic Azad University Tehran North Branch, Tehran, Iran.
| | - Mehrdad Mohammadpour Dehkordi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mohammad Hossein Asgarshamsi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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24
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Yilmaz B, Sharma H, Melekoglu E, Ozogul F. Recent developments in dairy kefir-derived lactic acid bacteria and their health benefits. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101592] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Xavier-Santos D, Padilha M, Fabiano GA, Vinderola G, Gomes Cruz A, Sivieri K, Costa Antunes AE. Evidences and perspectives of the use of probiotics, prebiotics, synbiotics, and postbiotics as adjuvants for prevention and treatment of COVID-19: A bibliometric analysis and systematic review. Trends Food Sci Technol 2022; 120:174-192. [PMID: 35002079 PMCID: PMC8720301 DOI: 10.1016/j.tifs.2021.12.033] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/03/2021] [Accepted: 12/28/2021] [Indexed: 02/09/2023]
Abstract
BACKGROUND Coronavirus disease-19 (COVID-19) is an infectious disease transmitted by the virus responsible for the severe acute respiratory syndrome 2 (SARS-CoV-2), which exhibit several clinical manifestations including gastrointestinal symptoms. SCOPE AND APPROACH This review aimed to provide insights and perspectives for the use of probiotics, prebiotics, synbiotics, and postbiotics as adjuvants for prevention/treatment and/or modulation of the microbiota in COVID-19 patients. Eighty-four studies published in the Scopus database from the onset of the pandemic until December 2021 were assessed and submitted to a bibliometric analysis adapted from VOSviewer software. KEY FINDINGS AND CONCLUSIONS Through bibliometric analysis, it might be suggested that the modulation of the gut/lung microbiome is promising as an adjuvant for the prevention/treatment of COVID-19 patients, due to immunomodulation properties related to probiotics and prebiotics. So far, few clinical studies involving the application of probiotics in COVID-19 patients have been completed, but reduction in the duration of the disease and the severity of symptoms as fatigue, olfactory dysfunction and breathlessness, nausea and vomiting and other gastrointestinal symptoms were some of the main findings. However, probiotics are not recommended to immunocompromised patients in corticosteroid therapy. The future perspectives point to the modulation of the intestinal microbiota by probiotics, prebiotics, synbiotics, and postbiotics represent a promising adjuvant approach for improving the health of patients with COVID-19.
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Affiliation(s)
- Douglas Xavier-Santos
- School of Applied Sciences (FCA), State University of Campinas, 1300 Pedro Zaccaria St, Zip Code 13484-350, Limeira, SP, Brazil
| | - Marina Padilha
- Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Zip Code 21941-902, Brazil
| | - Giovanna Alexandre Fabiano
- School of Applied Sciences (FCA), State University of Campinas, 1300 Pedro Zaccaria St, Zip Code 13484-350, Limeira, SP, Brazil
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Facultad de Ingeniería Química, Universidad Nacional Del Litoral, Santiago Del Estero 2829, Santa Fe, 3000, Argentina
| | - Adriano Gomes Cruz
- Department of Food, Federal Institute of Science and Technology of Rio de Janeiro (IFRJ), 121/125 Senador Furtado St, Zip Code 20270-021, Rio de Janeiro, RJ, Brazil
| | - Katia Sivieri
- Department of Food and Nutrition, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Rodovia Araraquara Jaú Km 1, Zip Code 14800-903, Araraquara, SP, Brazil
| | - Adriane Elisabete Costa Antunes
- School of Applied Sciences (FCA), State University of Campinas, 1300 Pedro Zaccaria St, Zip Code 13484-350, Limeira, SP, Brazil
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Khani N, Abedi Soleimani R, Noorkhajavi G, Abedi Soleimani A, Abbasi A, Homayouni Rad A. Postbiotics as Potential Promising Tools for SARS‐COV‐2 Disease Adjuvant Therapy. J Appl Microbiol 2022; 132:4097-4111. [DOI: 10.1111/jam.15457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/02/2022] [Accepted: 01/15/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Nader Khani
- Student Research Committee Tabriz University of Medical Sciences Tabriz Iran
- Department of Food Science and Technology Faculty of Nutrition & Food Sciences Nutrition Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Roya Abedi Soleimani
- Department of Food Science and Technology Faculty of Nutrition & Food Sciences Nutrition Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Ghasem Noorkhajavi
- Department of Medical Nanotechnology Tabriz University of Medical Sciences Tabriz Iran
| | - Azar Abedi Soleimani
- Faculty of Nursing & Midwifery Isfahan University of Medical Sciences Isfahan Iran
| | - Amin Abbasi
- Student Research Committee Department of Food Science and Technology National Nutrition and Food Technology Research Institute Faculty of Nutrition Science and Food Technology Shahid Beheshti University of Medical Sciences Tehran Iran
| | - Aziz Homayouni Rad
- Department of Food Science and Technology Faculty of Nutrition & Food Sciences Nutrition Research Center Tabriz University of Medical Sciences Tabriz Iran
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Moradi M, Golmohammadi R, Najafi A, Moosazadeh Moghaddam M, Fasihi-Ramandi M, Mirnejad R. A contemporary review on the important role of in silico approaches for managing different aspects of COVID-19 crisis. INFORMATICS IN MEDICINE UNLOCKED 2022; 28:100862. [PMID: 35079621 PMCID: PMC8776350 DOI: 10.1016/j.imu.2022.100862] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/05/2023] Open
Abstract
In the last century, the emergence of in silico tools has improved the quality of healthcare studies by providing high quality predictions. In the case of COVID-19, these tools have been advantageous for bioinformatics analysis of SARS-CoV-2 structures, studying potential drugs and introducing drug targets, investigating the efficacy of potential natural product components at suppressing COVID-19 infection, designing peptide-mimetic and optimizing their structure to provide a better clinical outcome, and repurposing of the previously known therapeutics. These methods have also helped medical biotechnologists to design various vaccines; such as multi-epitope vaccines using reverse vaccinology and immunoinformatics methods, among which some of them have showed promising results through in vitro, in vivo and clinical trial studies. Moreover, emergence of artificial intelligence and machine learning algorithms have helped to classify the previously known data and use them to provide precise predictions and make plan for future of the pandemic condition. At this contemporary review, by collecting related information from the collected literature on valuable data sources; such as PubMed, Scopus, and Web of Science, we tried to provide a brief outlook regarding the importance of in silico tools in managing different aspects of COVID-19 pandemic infection and how these methods have been helpful to biomedical researchers.
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Affiliation(s)
- Mohammad Moradi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Reza Golmohammadi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases (BRCGL), Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Mahdi Fasihi-Ramandi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Mirnejad
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Nguyen QV, Chong LC, Hor YY, Lew LC, Rather IA, Choi SB. Role of Probiotics in the Management of COVID-19: A Computational Perspective. Nutrients 2022; 14:274. [PMID: 35057455 PMCID: PMC8781206 DOI: 10.3390/nu14020274] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) was declared a pandemic at the beginning of 2020, causing millions of deaths worldwide. Millions of vaccine doses have been administered worldwide; however, outbreaks continue. Probiotics are known to restore a stable gut microbiota by regulating innate and adaptive immunity within the gut, demonstrating the possibility that they may be used to combat COVID-19 because of several pieces of evidence suggesting that COVID-19 has an adverse impact on gut microbiota dysbiosis. Thus, probiotics and their metabolites with known antiviral properties may be used as an adjunctive treatment to combat COVID-19. Several clinical trials have revealed the efficacy of probiotics and their metabolites in treating patients with SARS-CoV-2. However, its molecular mechanism has not been unraveled. The availability of abundant data resources and computational methods has significantly changed research finding molecular insights between probiotics and COVID-19. This review highlights computational approaches involving microbiome-based approaches and ensemble-driven docking approaches, as well as a case study proving the effects of probiotic metabolites on SARS-CoV-2.
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Affiliation(s)
- Quang Vo Nguyen
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Wilayah Persekutuan, Kuala Lumpur 50490, Malaysia;
| | - Li Chuin Chong
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul 34820, Turkey;
| | - Yan-Yan Hor
- Department of Biotechnology, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Gyeongbuk, Korea;
| | - Lee-Ching Lew
- Probionic Corporation, Jeonbuk Institute for Food-Bioindustry, Jeonju 54810, Korea;
| | - Irfan A. Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Sy-Bing Choi
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Wilayah Persekutuan, Kuala Lumpur 50490, Malaysia;
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29
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Mörschbächer AP, Granada CE. MAPPING THE WORLDWIDE KNOWLEDGE OF ANTIMICROBIAL SUBSTANCES PRODUCED BY Lactobacillus spp.: A BIBLIOMETRIC ANALYSIS. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Tian T, Xie W, Liu L, Fan S, Zhang H, Qin Z, Yang C. Industrial application of antimicrobial peptides based on their biological activity and structure-activity relationship. Crit Rev Food Sci Nutr 2021:1-16. [PMID: 34955061 DOI: 10.1080/10408398.2021.2019673] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Last several years, a rapid increase in drug resistance to traditional antibiotics has driven the emergence and development of antimicrobial peptides (AMPs). AMPs have also gained considerable attention from scientists due to their high potency in combatting infectious pathogens. A subset of analogues and their derivatives with specific targets have been successfully designed based on natural peptide patterns. In this review, scientific knowledge on the mechanisms of action related to biological activity and structure-activity relationship (SAR) of AMPs are summarized, and the biological applications in several important fields are critically discussed. SAR shows that the positive charge, secondary structure, special amino acid residues, hydrophobicity, and helicity of AMPs are closely related to their biological activities. The combination of nanotechnology, bioinformatics, and genetic engineering can accelerate to achieve the application of AMPs as effective, safe, economical, and nonresistant antimicrobial agents in medicine, the food and feed industries, and agriculture in coming years. Given the intense interest in AMPs, further investigations are needed in the future to evaluate the specific structure and function that make their use favorable in several industries. This review may provide a comprehensive reference for future studies on chemical modifications, mechanistic exploration, and applications of AMPs.
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Affiliation(s)
- Tiantian Tian
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong 519087, China
| | - Wansheng Xie
- Hainan Center for Drug and Medical Device Evaluation and Service, Hainan Provincial Drug Administration, Haikou, Hainan, China
| | - Luxuan Liu
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong 519087, China
| | - Siting Fan
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong 519087, China
| | - Heqian Zhang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong 519087, China
| | - Zhiwei Qin
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong 519087, China
| | - Chao Yang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong 519087, China.,State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied research in Medicine and Health, University of Science and Technology, Taipa, Macao, China
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31
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Razali R, Asis H, Budiman C. Structure-Function Characteristics of SARS-CoV-2 Proteases and Their Potential Inhibitors from Microbial Sources. Microorganisms 2021; 9:2481. [PMID: 34946083 PMCID: PMC8706127 DOI: 10.3390/microorganisms9122481] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is considered the greatest challenge to the global health community of the century as it continues to expand. This has prompted immediate urgency to discover promising drug targets for the treatment of COVID-19. The SARS-CoV-2 viral proteases, 3-chymotrypsin-like protease (3CLpro) and papain-like cysteine protease (PLpro), have become the promising target to study due to their essential functions in spreading the virus by RNA transcription, translation, protein synthesis, processing and modification, virus replication, and infection of the host. As such, understanding of the structure and function of these two proteases is unavoidable as platforms for the development of inhibitors targeting this protein which further arrest the infection and spread of the virus. While the abundance of reports on the screening of natural compounds such as SARS-CoV-2 proteases inhibitors are available, the microorganisms-based compounds (peptides and non-peptides) remain less studied. Indeed, microorganisms-based compounds are also one of the potent antiviral candidates against COVID-19. Microbes, especially bacteria and fungi, are other resources to produce new drugs as well as nucleosides, nucleotides, and nucleic acids. Thus, we have compiled various reported literature in detail on the structures, functions of the SARS-CoV-2 proteases, and potential inhibitors from microbial sources as assistance to other researchers working with COVID-19. The compounds are also compared to HIV protease inhibitors which suggested the microorganisms-based compounds are advantageous as SARS-CoV2 proteases inhibitors. The information should serve as a platform for further development of COVID-19 drug design strategies.
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Affiliation(s)
| | | | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia; (R.R.); (H.A.)
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32
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Rima M, Rima M, Fajloun Z, Sabatier JM, Bechinger B, Naas T. Antimicrobial Peptides: A Potent Alternative to Antibiotics. Antibiotics (Basel) 2021; 10:1095. [PMID: 34572678 PMCID: PMC8466391 DOI: 10.3390/antibiotics10091095] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/07/2023] Open
Abstract
Antimicrobial peptides constitute one of the most promising alternatives to antibiotics since they could be used to treat bacterial infections, especially those caused by multidrug-resistant pathogens. Many antimicrobial peptides, with various activity spectra and mechanisms of actions, have been described. This review focuses on their use against ESKAPE bacteria, especially in biofilm treatments, their synergistic activity, and their application as prophylactic agents. Limitations and challenges restricting therapeutic applications are highlighted, and solutions for each challenge are evaluated to analyze whether antimicrobial peptides could replace antibiotics in the near future.
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Affiliation(s)
- Mariam Rima
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, 94270 Le Kremlin-Bicetre, France;
| | - Mohamad Rima
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon; (M.R.); (Z.F.)
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon; (M.R.); (Z.F.)
- Department of Biology, Faculty of Sciences III, Lebanese University, Tripoli 1300, Lebanon
| | - Jean-Marc Sabatier
- Institut de Neuro Physiopathologie, UMR7051, Aix-Marseille Université, Faculté de Pharmacie, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Burkhard Bechinger
- Institut de Chimie de Strasbourg, CNRS, UMR7177, University of Strasbourg, 67008 Strasbourg, France;
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Thierry Naas
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, 94270 Le Kremlin-Bicetre, France;
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicetre, France
- French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, 94270 Le Kremlin-Bicetre, France
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33
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Kefir as a Functional Beverage Gaining Momentum towards Its Health Promoting Attributes. BEVERAGES 2021. [DOI: 10.3390/beverages7030048] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The consumption of fermented foods posing health-promoting attributes is a rising global trend. In this manner, fermented dairy products represent a significant subcategory of functional foods with established positive health benefits. Likewise, kefir—a fermented milk product manufactured from kefir grains—has been reported by many studies to be a probiotic drink with great potential in health promotion. Existing research data link regular kefir consumption with a wide range of health-promoting attributes, and more recent findings support the link between kefir’s probiotic strains and its bio-functional metabolites in the enhancement of the immune system, providing significant antiviral effects. Although it has been consumed for thousands of years, kefir has recently gained popularity in relation to novel biotechnological applications, with different fermentation substrates being tested as non-dairy functional beverages. The present review focuses on the microbiological composition of kefir and highlights novel applications associated with its fermentation capacity. Future prospects relating to kefir’s capacity for disease prevention are also addressed and discussed.
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Barbosa J, Albano H, Silva B, Almeida MH, Nogueira T, Teixeira P. Characterization of a Lactiplantibacillus plantarum R23 Isolated from Arugula by Whole-Genome Sequencing and Its Bacteriocin Production Ability. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:5515. [PMID: 34063896 PMCID: PMC8196627 DOI: 10.3390/ijerph18115515] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Accepted: 05/17/2021] [Indexed: 01/03/2023]
Abstract
Lactiplantibacillus plantarum is one of the lactic acid bacteria species most used as probiotics and starter cultures in food production. Bacteriocin-producers Lpb. plantarum are also promising natural food preservatives. This study aimed to characterize Lpb. plantarum R23 and its bacteriocins (R23 bacteriocins). The genome sequence of Lpb. plantarum R23 was obtained by whole-genome sequencing (WGS) in an Illumina NovaSeq platform. The activity of Lpb. plantarum R23-produced bacteriocin against two Listeria monocytogenes strains (L7946 and L7947) was evaluated, and its molecular size was determined by tricine-SDS-PAGE. No virulence or antibiotic resistance genes were detected. Four 100% identical proteins to the class II bacteriocins (Plantaricin E, Plantaricin F, Pediocin PA-1 (Pediocin AcH), and Coagulin A) were found by WGS analysis. The small (<6.5 kDa) R23 bacteriocins were stable at different pH values (ranging from 2 to 8), temperatures (between 4 and 100 °C), detergents (all, except Triton X-100 and Triton X-114 at 0.01 g/mL), and enzymes (catalase and α-amylase), did not adsorb to the producer cells, had a bacteriostatic mode of action and their maximum activity (AU/mL = 12,800) against two L. monocytogenes strains occurred between 15 and 21 h of Lpb. plantarum R23 growth. Lactiplantibacillus plantarum R23 showed to be a promising bio-preservative culture because, besides being safe, it produces a stable bacteriocin or bacteriocins (harbors genes encoding for the production of four) inhibiting pathogens as L. monocytogenes. Further studies in different food matrices are required to confirm this hypothesis and its suitability as a future starter culture.
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Affiliation(s)
- Joana Barbosa
- CBQF-Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4169-005 Porto, Portugal;
| | - Helena Albano
- CBQF-Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4169-005 Porto, Portugal;
| | - Beatriz Silva
- Colégio de São Gonçalo, 4600-014 Amarante, Portugal;
| | | | - Teresa Nogueira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., 2780-157 Oeiras and 4485-655 Vairão, Portugal;
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Paula Teixeira
- CBQF-Centro de Biotecnologia e Química Fina–Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, 4169-005 Porto, Portugal;
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