1
|
Gok B, Budama-Kilinc Y, Kecel-Gunduz S. Anti-aging activity of Syn-Ake peptide by in silico approaches and in vitro tests. J Biomol Struct Dyn 2024; 42:5015-5029. [PMID: 37349941 DOI: 10.1080/07391102.2023.2223681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
The increase in the aging population worldwide has led scientists to turn to research to prevent the aging process. In this context, synthetic peptides emerge as candidate molecules for developing new anti-aging products. This study aims to investigate the possible interactions of Syn-Ake, a synthetic peptide, with matrix metalloproteinases (MMPs) and Sirtuin 1 (SIRT1), which are the targets of anti-aging activities with in silico approaches, and to determine the antioxidant activity, and safety profile of the peptide by in vitro methods such as cytotoxicity (MTT) and genotoxicity (Ames) tests. The molecular docking study showed that the docking score energy of MMP receptors was in the order of MMP-13 < MMP-8 < MMP-1. Syn-Ake peptide provided the lowest and the most stable binding to the SIRT1 receptor at -9.32 kcal/mol. Binding interaction and protein-ligand stability of Syn-Ake with MMPs and SIRT1 in a dynamic system were predicted by 50 ns molecular dynamic (MD) simulation studies. The MD results showed that the Syn-Ake peptide remained stable in the active site of MMP-13 and SIRT1 receptors during 50 ns simulations. In addition, the antioxidant activity of Syn-Ake was investigated using diphenyl-2-picril-hydrazine (DPPH) method since it is crucial to remove free radicals that are effective in skin aging. The results revealed the concentration-dependent increased DPPH radical scavenging activity of the peptide. Finally, the safety of the Syn-Ake was investigated, and the safe dose of the peptide was determined. In conclusion, in silico and in vitro analyses show that the Syn-Ake peptide may hold promise in anti-aging formulations with its high efficacy and safety profile.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Bahar Gok
- Graduate School of Natural and Applied Science, Yildiz Technical University, Istanbul, Turkey
| | - Yasemin Budama-Kilinc
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey
| | - Serda Kecel-Gunduz
- Faculty of Science, Department of Physics, Istanbul University, Istanbul, Turkey
| |
Collapse
|
2
|
Moreira L, Guimarães NM, Santos RS, Loureiro JA, Pereira MC, Azevedo NF. Promising strategies employing nucleic acids as antimicrobial drugs. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102122. [PMID: 38333674 PMCID: PMC10850860 DOI: 10.1016/j.omtn.2024.102122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Antimicrobial resistance (AMR) is a growing concern because it causes microorganisms to develop resistance to drugs commonly used to treat infections. This results in increased difficulty in treating infections, leading to higher mortality rates and significant economic effects. Investing in new antimicrobial agents is, therefore, necessary to prevent and control AMR. Antimicrobial nucleic acids have arisen as potential key players in novel therapies for AMR infections. They have been designed to serve as antimicrobials and to act as adjuvants to conventional antibiotics or to inhibit virulent mechanisms. This new category of antimicrobial drugs consists of antisense oligonucleotides and oligomers, DNAzymes, and transcription factor decoys, differing in terms of structure, target molecules, and mechanisms of action. They are synthesized using nucleic acid analogs to enhance their resistance to nucleases. Because bacterial envelopes are generally impermeable to oligonucleotides, delivery into the cytoplasm typically requires the assistance of nanocarriers, which can affect their therapeutic potency. Given that numerous factors contribute to the success of these antimicrobial drugs, this review aims to provide a summary of the key advancements in the use of oligonucleotides for treating bacterial infections. Their mechanisms of action and the impact of factors such as nucleic acid design, target sequence, and nanocarriers on the antimicrobial potency are discussed.
Collapse
Affiliation(s)
- Luís Moreira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno M. Guimarães
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Rita S. Santos
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana A. Loureiro
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Maria C. Pereira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| |
Collapse
|
3
|
Liu Y, Long S, Wang H, Wang Y. Biofilm therapy for chronic wounds. Int Wound J 2024; 21:e14667. [PMID: 38339793 PMCID: PMC10858329 DOI: 10.1111/iwj.14667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 02/12/2024] Open
Abstract
Chronic wounds have been a major factor of serious harm to global public health. At present, it is known that almost all chronic wounds contain biofilms, which seriously hinder the healing process. Removal of biofilms can effectively promote the healing of chronic wounds. As the study of wound biofilms deepens, many new treatment methods have emerged, thus bringing revolutionary means for the treatment of chronic wound biofilm. This review summarizes various methods for the treatment of chronic wound biofilm worldwide to provide a theoretical summary and practical basis for the selection of suitable wound biofilm treatment methods in clinical practice.
Collapse
Affiliation(s)
- Yang Liu
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of ChengduAffiliated Hospital of Southwest Jiaotong UniversityChengduChina
| | - Shengyong Long
- Department of TraumatologyTongren People's HospitalTongrenChina
| | - Hanfeng Wang
- Plastic Surgery DepartmentXi'an International Medical Center HospitalXi'anChina
| | - Yan Wang
- Center of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, The Third People's Hospital of ChengduAffiliated Hospital of Southwest Jiaotong UniversityChengduChina
- Medical Research Center, The Third People's Hospital of ChengduAffiliated Hospital of Southwest Jiaotong UniversityChengduChina
| |
Collapse
|
4
|
Plotniece A, Sobolev A, Supuran CT, Carta F, Björkling F, Franzyk H, Yli-Kauhaluoma J, Augustyns K, Cos P, De Vooght L, Govaerts M, Aizawa J, Tammela P, Žalubovskis R. Selected strategies to fight pathogenic bacteria. J Enzyme Inhib Med Chem 2023; 38:2155816. [PMID: 36629427 PMCID: PMC9848314 DOI: 10.1080/14756366.2022.2155816] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Natural products and analogues are a source of antibacterial drug discovery. Considering drug resistance levels emerging for antibiotics, identification of bacterial metalloenzymes and the synthesis of selective inhibitors are interesting for antibacterial agent development. Peptide nucleic acids are attractive antisense and antigene agents representing a novel strategy to target pathogens due to their unique mechanism of action. Antisense inhibition and development of antisense peptide nucleic acids is a new approach to antibacterial agents. Due to the increased resistance of biofilms to antibiotics, alternative therapeutic options are necessary. To develop antimicrobial strategies, optimised in vitro and in vivo models are needed. In vivo models to study biofilm-related respiratory infections, device-related infections: ventilator-associated pneumonia, tissue-related infections: chronic infection models based on alginate or agar beads, methods to battle biofilm-related infections are discussed. Drug delivery in case of antibacterials often is a serious issue therefore this review includes overview of drug delivery nanosystems.
Collapse
Affiliation(s)
- Aiva Plotniece
- Latvian Institute of Organic Synthesis, Riga, Latvia,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Riga Stradiņš University, Riga, Latvia,CONTACT Aiva Plotniece Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fabrizio Carta
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Jari Yli-Kauhaluoma
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Koen Augustyns
- Infla-Med, Centre of Excellence, University of Antwerp, Antwerp, Belgium,Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Linda De Vooght
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Matthias Govaerts
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Juliana Aizawa
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Raivis Žalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia,Faculty of Materials Science and Applied Chemistry, Institute of Technology of Organic Chemistry, Riga Technical University, Riga, Latvia
| |
Collapse
|
5
|
Selvaraj SP, Chen JY. Conjugation of antimicrobial peptides to enhance therapeutic efficacy. Eur J Med Chem 2023; 259:115680. [PMID: 37515922 DOI: 10.1016/j.ejmech.2023.115680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/05/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023]
Abstract
The growing prevalence of antimicrobial resistance (AMR) has brought with it a continual increase in the numbers of deaths from multidrug-resistant (MDR) infections. Since the current arsenal of antibiotics has become increasingly ineffective, there exists an urgent need for discovery and development of novel antimicrobials. Antimicrobial peptides (AMPs) are considered to be a promising class of molecules due to their broad-spectrum activities and low resistance rates compared with other types of antibiotics. Since AMPs also often play major roles in elevating the host immune response, the molecules may also be called "host defense peptides." Despite the great promise of AMPs, the majority remain unsuitable for clinical use due to issues of structural instability, degradation by proteases, and/or toxicity to host cells. Moreover, AMP activities in vivo can be influenced by many factors, such as interaction with blood and serum biomolecules, physiological salt concentrations or different pH values. To overcome these limitations, structural modifications can be made to the AMP. Among several modifications, physical and chemical conjugation of AMP to other biomolecules is widely considered an effective strategy. In this review, we discuss structural modification strategies related to conjugation of AMPs and their possible effects on mode of action. The conjugation of fatty acids, glycans, antibiotics, photosensitizers, polymers, nucleic acids, nanoparticles, and immobilization to biomaterials are highlighted.
Collapse
Affiliation(s)
- Sanjay Prasad Selvaraj
- Molecular and Biological Agricultural Science Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Jyh-Yih Chen
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd, Jiaushi, Ilan, 262, Taiwan; The iEGG and Animal Biotechnology Center and the Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, 402, Taiwan.
| |
Collapse
|
6
|
Qun T, Zhou T, Hao J, Wang C, Zhang K, Xu J, Wang X, Zhou W. Antibacterial activities of anthraquinones: structure-activity relationships and action mechanisms. RSC Med Chem 2023; 14:1446-1471. [PMID: 37593578 PMCID: PMC10429894 DOI: 10.1039/d3md00116d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/24/2023] [Indexed: 08/19/2023] Open
Abstract
With the increasing prevalence of untreatable infections caused by antibiotic-resistant bacteria, the discovery of new drugs from natural products has become a hot research topic. The antibacterial activity of anthraquinones widely distributed in traditional Chinese medicine has attracted much attention. Herein, the structure and activity relationships (SARs) of anthraquinones as bacteriostatic agents are reviewed and elucidated. The substituents of anthraquinone and its derivatives are closely related to their antibacterial activities. The stronger the polarity of anthraquinone substituents is, the more potent the antibacterial effects appear. The presence of hydroxyl groups is not necessary for the antibacterial activity of hydroxyanthraquinone derivatives. Substitution of di-isopentenyl groups can improve the antibacterial activity of anthraquinone derivatives. The rigid plane structure of anthraquinone lowers its water solubility and results in the reduced activity. Meanwhile, the antibacterial mechanisms of anthraquinone and its analogs are explored, mainly including biofilm formation inhibition, destruction of the cell wall, endotoxin inhibition, inhibition of nucleic acid and protein synthesis, and blockage of energy metabolism and other substances.
Collapse
Affiliation(s)
- Tang Qun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
| | - Tiantian Zhou
- School of Chinese Materia Medica, Guangdong Pharmaceutical University 440113 Guangzhou China
| | - Jiongkai Hao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
| | - Chunmei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
- Key laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai Research Institute, Chinese Academy of Agricultural Sciences Shanghai 200241 China
| | - Keyu Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
- Key laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai Research Institute, Chinese Academy of Agricultural Sciences Shanghai 200241 China
| | - Jing Xu
- Huanghua Agricultural and Rural Development Bureau Bohai New Area 061100 Hebei China
| | - Xiaoyang Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
- Key laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai Research Institute, Chinese Academy of Agricultural Sciences Shanghai 200241 China
| | - Wen Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences 200241 Shanghai China
- Key laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs, Shanghai Research Institute, Chinese Academy of Agricultural Sciences Shanghai 200241 China
| |
Collapse
|
7
|
Tekintaş Y, Temel A. Antisense oligonucleotides: a promising therapeutic option against infectious diseases. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:1-39. [PMID: 37395450 DOI: 10.1080/15257770.2023.2228841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/19/2023] [Indexed: 07/04/2023]
Abstract
Infectious diseases have been one of the biggest health problems of humanity for centuries. Nucleic acid-based therapeutics have received attention in recent years with their effectiveness in the treatment of various infectious diseases and vaccine development studies. This review aims to provide a comprehensive understanding of the basic properties underlying the mechanism of antisense oligonucleotides (ASOs), their applications, and their challenges. The efficient delivery of ASOs is the greatest challenge for their therapeutic success, but this problem is overcome with new-generation antisense molecules developed with chemical modifications. The types, carrier molecules, and gene regions targeted by sequences have been summarized in detail. Research and development of antisense therapy is still in its infancy; however, gene silencing therapies appear to have the potential for faster and longer-lasting activity than conventional treatment strategies. On the other hand, realizing the potential of antisense therapy will require a large initial economic investment to ascertain the pharmacological properties and learn how to optimize them. The ability of ASOs to be rapidly designed and synthesized to target different microbes can reduce drug discovery time from 6 years to 1 year. Since ASOs are not particularly affected by resistance mechanisms, they come to the fore in the fight against antimicrobial resistance. The design-based flexibility of ASOs has enabled it to be used for different types of microorganisms/genes and successful in vitro and in vivo results have been revealed. The current review summarized a comprehensive understanding of ASO therapy in combating bacterial and viral infections.
Collapse
Affiliation(s)
- Yamaç Tekintaş
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Türkiye
| | - Aybala Temel
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Türkiye
| |
Collapse
|
8
|
Kifayat S, Yele V, Ashames A, Sigalapalli DK, Bhandare RR, Shaik AB, Nasipireddy V, Sanapalli BKR. Filamentous temperature sensitive mutant Z: a putative target to combat antibacterial resistance. RSC Adv 2023; 13:11368-11384. [PMID: 37057268 PMCID: PMC10089256 DOI: 10.1039/d3ra00013c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
In the pre-antibiotic era, common bacterial infections accounted for high mortality and morbidity. Moreover, the discovery of penicillin in 1928 marked the beginning of an antibiotic revolution, and this antibiotic era witnessed the discovery of many novel antibiotics, a golden era. However, the misuse or overuse of these antibiotics, natural resistance that existed even before the antibiotics were discovered, genetic variations in bacteria, natural selection, and acquisition of resistance from one species to another consistently increased the resistance to the existing antibacterial targets. Antibacterial resistance (ABR) is now becoming an ever-increasing concern jeopardizing global health. Henceforth, there is an urgent unmet need to discover novel compounds to combat ABR, which act through untapped pathways/mechanisms. Filamentous Temperature Sensitive mutant Z (FtsZ) is one such unique target, a tubulin homolog involved in developing a cytoskeletal framework for the cytokinetic ring. Additionally, its pivotal role in bacterial cell division and the lack of homologous structural protein in mammals makes it a potential antibacterial target for developing novel molecules. Approximately 2176 X-crystal structures of FtsZ were available, which initiated the research efforts to develop novel antibacterial agents. The literature has reported several natural, semisynthetic, peptides, and synthetic molecules as FtsZ inhibitors. This review provides valuable insights into the basic crystal structure of FtsZ, its inhibitors, and their inhibitory activities. This review also describes the available in vitro detection and quantification methods of FtsZ-drug complexes and the various approaches for determining drugs targeting FtsZ polymerization.
Collapse
Affiliation(s)
- Sumaiya Kifayat
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India +91-9291661992
| | - Vidyasrilekha Yele
- Department of Pharmaceutical Chemistry, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India
| | - Akram Ashames
- College of Pharmacy & Health Sciences, Ajman University PO Box 340 Ajman United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University PO Box 340 Ajman United Arab Emirates +97167056240
| | - Dilep Kumar Sigalapalli
- Department of Pharmaceutical Chemistry, Vignan Pharmacy College, Jawaharlal Nehru Technological University Vadlamudi 522213 Andhra Pradesh India
| | - Richie R Bhandare
- College of Pharmacy & Health Sciences, Ajman University PO Box 340 Ajman United Arab Emirates
- Center of Medical and Bio-allied Health Sciences Research, Ajman University PO Box 340 Ajman United Arab Emirates +97167056240
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada Chebrolu Guntur 522212 Andhra Pradesh India
| | | | - Bharat Kumar Reddy Sanapalli
- Department of Pharmacology, NIMS Institute of Pharmacy, NIMS University Rajasthan Jaipur 303121 India +91-9291661992
| |
Collapse
|
9
|
Zhao A, Sun J, Liu Y. Understanding bacterial biofilms: From definition to treatment strategies. Front Cell Infect Microbiol 2023; 13:1137947. [PMID: 37091673 PMCID: PMC10117668 DOI: 10.3389/fcimb.2023.1137947] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/09/2023] [Indexed: 04/08/2023] Open
Abstract
Bacterial biofilms are complex microbial communities encased in extracellular polymeric substances. Their formation is a multi-step process. Biofilms are a significant problem in treating bacterial infections and are one of the main reasons for the persistence of infections. They can exhibit increased resistance to classical antibiotics and cause disease through device-related and non-device (tissue) -associated infections, posing a severe threat to global health issues. Therefore, early detection and search for new and alternative treatments are essential for treating and suppressing biofilm-associated infections. In this paper, we systematically reviewed the formation of bacterial biofilms, associated infections, detection methods, and potential treatment strategies, aiming to provide researchers with the latest progress in the detection and treatment of bacterial biofilms.
Collapse
Affiliation(s)
- Ailing Zhao
- Department of Gastroenterology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
| | - Jiazheng Sun
- Department of Vasculocardiology, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Yipin Liu
- Department of Gastroenterology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
- *Correspondence: Yipin Liu,
| |
Collapse
|
10
|
Ciulla MG, Gelain F. Structure-activity relationships of antibacterial peptides. Microb Biotechnol 2023; 16:757-777. [PMID: 36705032 PMCID: PMC10034643 DOI: 10.1111/1751-7915.14213] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/08/2022] [Accepted: 01/01/2023] [Indexed: 01/28/2023] Open
Abstract
Antimicrobial peptides play a crucial role in innate immunity, whose components are mainly peptide-based molecules with antibacterial properties. Indeed, the exploration of the immune system over the past 40 years has revealed a number of natural peptides playing a pivotal role in the defence mechanisms of vertebrates and invertebrates, including amphibians, insects, and mammalians. This review provides a discussion regarding the antibacterial mechanisms of peptide-based agents and their structure-activity relationships (SARs) with the aim of describing a topic that is not yet fully explored. Some growing evidence suggests that innate immunity should be strongly considered for the development of novel antibiotic peptide-based libraries. Also, due to the constantly rising concern of antibiotic resistance, the development of new antibiotic drugs is becoming a priority of global importance. Hence, the study and the understanding of defence phenomena occurring in the immune system may inspire the development of novel antibiotic compound libraries and set the stage to overcome drug-resistant pathogens. Here, we provide an overview of the importance of peptide-based antibacterial sources, focusing on accurately selected molecular structures, their SARs including recently introduced modifications, their latest biotechnology applications, and their potential against multi-drug resistant pathogens. Last, we provide cues to describe how antibacterial peptides show a better scope of action selectivity than several anti-infective agents, which are characterized by non-selective activities and non-targeted actions toward pathogens.
Collapse
Affiliation(s)
- Maria Gessica Ciulla
- Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Center for Nanomedicine and Tissue Engineering (CNTE), ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Fabrizio Gelain
- Institute for Stem-Cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Center for Nanomedicine and Tissue Engineering (CNTE), ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| |
Collapse
|
11
|
Yokoi Y, Kawabuchi Y, Zulmajdi AA, Tanaka R, Shibata T, Muraoka T, Mori T. Cell-Penetrating Peptide-Peptide Nucleic Acid Conjugates as a Tool for Protein Functional Elucidation in the Native Bacterium. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248944. [PMID: 36558072 PMCID: PMC9788395 DOI: 10.3390/molecules27248944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Approximately 30% or more of the total proteins annotated from sequenced bacteria genomes are annotated as hypothetical or uncharacterized proteins. However, elucidation on the function of these proteins is hindered by the lack of simple and rapid screening methods, particularly with novel or hard-to-transform bacteria. In this report, we employed cell-penetrating peptide (CPP) -peptide nucleotide acid (PNA) conjugates to elucidate the function of such uncharacterized proteins in vivo within the native bacterium. Paenibacillus, a hard-to-transform bacterial genus, was used as a model. Two hypothetical genes showing amino acid sequence similarity to ι-carrageenases, termed cgiA and cgiB, were identified from the draft genome of Paenibacillus sp. strain YYML68, and CPP-PNA probes targeting the mRNA of the acyl carrier protein gene, acpP, and the two ι-carrageenase candidate genes were synthesized. Upon direct incubation of CPP-PNA targeting the mRNA of the acpP gene, we successfully observed growth inhibition of strain YYML68 in a concentration-dependent manner. Similarly, both the function of the candidate ι-carrageenases were also inhibited using our CPP-PNA probes allowing for the confirmation and characterization of these hypothetical proteins. In summary, we believe that CPP-PNA conjugates can serve as a simple and efficient alternative approach to characterize proteins in the native bacterium.
Collapse
Affiliation(s)
- Yasuhito Yokoi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Yugo Kawabuchi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Abdullah Adham Zulmajdi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Reiji Tanaka
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya-cho, Tsu-shi 514-8507, Mie, Japan
| | - Toshiyuki Shibata
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya-cho, Tsu-shi 514-8507, Mie, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
| | - Tetsushi Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei-shi 184-8588, Tokyo, Japan
- Correspondence:
| |
Collapse
|
12
|
Konwar AN, Hazarika SN, Bharadwaj P, Thakur D. Emerging Non-Traditional Approaches to Combat Antibiotic Resistance. Curr Microbiol 2022; 79:330. [PMID: 36155858 PMCID: PMC9510247 DOI: 10.1007/s00284-022-03029-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022]
Abstract
An increasing number of bacterial pathogens are acquiring resistance to the commonly used antibiotics. This has spurred a global threat leading to a resistance era and has penetrated the consciousness of the common people and the clinicians alike. The delay in discovering new antibiotics has exacerbated the resistance problem, forcing researchers to focus on unconventional antimicrobial therapeutics that differ from conventional antibiotics. Alternative therapies have emerged in recent years, including antimicrobial peptides, phage therapy, efflux pump inhibitors, antibodies, and immunomodulatory agents, which have produced impressive results in both laboratory and in clinical trials. Additionally, ultra-narrow-spectrum therapeutics such as CRISPR-Cas system and peptide nucleic acids aided in the development of sequence-specific antimicrobials. Moreover, combinatorial therapies that combine these new approaches have been efficient enough to get approval for clinical use and have accelerated the discovery of novel combination approaches that enhance the performance of already in-use antibiotics. In this review, we provide an overview of these approaches along with studies that focus on the uncharted microbial territories that have been able to deliver some of the important new antibiotics of recent times. It is hoped that the information gathered in this article will provide an update on the current antibiotic resistance threat and encourage profound research.
Collapse
Affiliation(s)
- Aditya Narayan Konwar
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam, 781035, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shabiha Nudrat Hazarika
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam, 781035, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam, 781001, India
| | - Pranami Bharadwaj
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam, 781035, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debajit Thakur
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Studies in Science and Technology, Guwahati, Assam, 781035, India.
| |
Collapse
|
13
|
Popella L, Jung J, Do PT, Hayward RJ, Barquist L, Vogel J. Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli. Nucleic Acids Res 2022; 50:6435-6452. [PMID: 35687096 PMCID: PMC9226493 DOI: 10.1093/nar/gkac362] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) that target mRNAs of essential bacterial genes exhibit specific bactericidal effects in several microbial species, but our mechanistic understanding of PNA activity and their target gene spectrum is limited. Here, we present a systematic analysis of PNAs targeting 11 essential genes with varying expression levels in uropathogenic Escherichia coli (UPEC). We demonstrate that UPEC is susceptible to killing by peptide-conjugated PNAs, especially when targeting the widely-used essential gene acpP. Our evaluation yields three additional promising target mRNAs for effective growth inhibition, i.e.dnaB, ftsZ and rpsH. The analysis also shows that transcript abundance does not predict target vulnerability and that PNA-mediated growth inhibition is not universally associated with target mRNA depletion. Global transcriptomic analyses further reveal PNA sequence-dependent but also -independent responses, including the induction of envelope stress response pathways. Importantly, we show that 9mer PNAs are generally as effective in inhibiting bacterial growth as their 10mer counterparts. Overall, our systematic comparison of a range of PNAs targeting mRNAs of different essential genes in UPEC suggests important features for PNA design, reveals a general bacterial response to PNA conjugates and establishes the feasibility of using PNA antibacterials to combat UPEC.
Collapse
Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany
| | - Phuong Thao Do
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
| | - Regan J Hayward
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080, Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080, Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080, Würzburg, Germany
| |
Collapse
|
14
|
Potentiating the Anti-Tuberculosis Efficacy of Peptide Nucleic Acids through Combinations with Permeabilizing Drugs. Microbiol Spectr 2022; 10:e0126221. [PMID: 35171048 PMCID: PMC8849056 DOI: 10.1128/spectrum.01262-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The emergence of antimicrobial resistance warrants for the development of improved treatment approaches. In this regard, peptide nucleic acids (PNAs) have shown great promise, exhibiting antibiotic properties through the targeting of cellular nucleic acids. We aimed to study the efficacy of PNA as an anti-tuberculosis agent. Since the efficacy of PNA is limited by its low penetration into the cell, we also investigated combinatorial treatments using permeabilizing drugs to improve PNA efficacy. Various concentrations of anti-inhA PNA, permeabilizing drugs, and their combinations were screened against extracellular and intracellular mycobacteria.0.625 to 5 μM anti-inhA PNA was observed to merely inhibit the growth of extracellular M. smegmatis, while low intracellular bacterial load was reduced by 2 or 2.5 log-fold when treated with 2.5 or 5 μM PNA, respectively. Anti-inhA PNA against M. tuberculosis H37Ra exhibited bactericidal properties at 2.5 and 5 μM and enabled a slight reduction in intracellular M. tuberculosis at concentrations from 2.5 to 20 μM. Of the permeabilizing drugs tested, ethambutol showed the most permeabilizing potential and ultimately potentiated anti-inhA PNA to the greatest extent, reducing its efficacious concentration to 1.25 μM against both M. smegmatis and M. tuberculosis. Furthermore, an enhanced clearance of 1.3 log-fold was observed for ethambutol-anti-inhA PNA combinations against intracellular M. tuberculosis. Thus, permeabilizing drug-PNA combinations indeed exhibit improved efficacies. We therefore propose that anti-inhA PNA could improve therapy even when applied in minute doses as an addition to the current anti-tuberculosis drug regimen. IMPORTANCE Peptide nucleic acids have great potential in therapeutics as anti-gene/anti-sense agents. However, their limited uptake in cells has curtailed their widespread application. Through this study, we explore a PNA-drug combinatorial strategy to improve the efficacy of PNAs and reduce their effective concentrations. This work also focuses on improving tuberculosis treatment, which is hindered by the emergence of antimicrobial-resistant strains of Mycobacterium tuberculosis. It is observed that the antibacterial efficacy of anti-inhA PNA is enhanced when it is combined with permeabilizing drugs, particularly ethambutol. This indicates that the addition of even small concentrations of anti-inhA PNA to the current TB regimen could potentiate their therapeutic efficiency. We hypothesize that this system would also overcome isoniazid resistance, since the resistance mutations lie outside the designed anti-inhA PNA target site.
Collapse
|
15
|
Akpınar Kankaya D, Tuncer Y. Detection of Virulence Factors, Biofilm Formation and Biogenic Amine Production in
Vancomycin‐Resistant
Lactic Acid Bacteria (
VRLAB
) Isolated From Foods of Animal Origin. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16423] [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)
- Didem Akpınar Kankaya
- Department of Food Technology, Gelendost Vocational School Isparta University of Applied Sciences Isparta Turkey
| | - Yasin Tuncer
- Department of Food Engineering, Faculty of Engineering Süleyman Demirel University Isparta Turkey
| |
Collapse
|
16
|
Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| |
Collapse
|
17
|
Ozma MA, Khodadadi E, Rezaee MA, Kamounah FS, Asgharzadeh M, Ganbarov K, Aghazadeh M, Yousefi M, Pirzadeh T, Kafil HS. Induction of proteome changes involved in biofilm formation of Enterococcus faecalis in response to gentamicin. Microb Pathog 2021; 157:105003. [PMID: 34087388 DOI: 10.1016/j.micpath.2021.105003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Enterococcus faecalis is a significant cause of nosocomial infections and other diseases, including endocarditis, bacteremia, and urinary tract infections. This microorganism forms biofilms to overcome difficult environmental conditions, such as lack of oxygen, lack of water, and the presence of antimicrobials. These biofilms make diseases difficult by changing their proteome contents, protecting the bacterium, and increasing their pathogenicity. This study aimed to evaluate gentamicin's effect on proteome changes and biofilm formation in E. faecalis. METHOD Twenty-five clinical isolates and one standard isolate were selected for the experiments. A label-free/gel-free proteomic and microtiter plate techniques were used to study proteome changes and biofilm formation, respectively. RESULTS Gentamicin significantly increased the biofilm formation in 62% of isolates and the rest of the isolates; no significant change was observed. The abundance of lactate utilization protein C, ribosomal RNA small subunit methyltransferase H, and protein translocase subunit SecA were increased. However, the abundances of proteins effective in cell division and metabolism, such as replication initiation protein and segregation and condensation protein A, were decreased. CONCLUSION The present study's findings exhibited that antibiotics might have adverse effects on treatment and increase microorganisms' pathogenicity. It was observed in gentamicin as induction of biofilm formation through different mechanisms, particularly changes in the expression of specific proteins in E. faecalis.
Collapse
Affiliation(s)
- Mahdi Asghari Ozma
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ehsaneh Khodadadi
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK- 2100, Copenhagen, Denmark
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mohammad Aghazadeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Pirzadeh
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
18
|
Hemmati F, Rezaee MA, Ebrahimzadeh S, Yousefi L, Nouri R, Kafil HS, Gholizadeh P. Novel Strategies to Combat Bacterial Biofilms. Mol Biotechnol 2021; 63:569-586. [PMID: 33914260 DOI: 10.1007/s12033-021-00325-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/09/2021] [Indexed: 12/15/2022]
Abstract
Biofilms are considered as a severe problem in the treatment of bacterial infections; their development causes some noticeable resistance to antibacterial agents. Biofilms are responsible for at least two-thirds of all infections, displaying promoted resistance to classical antibiotic treatments. Therefore, finding new alternative therapeutic approaches is essential for the treatment and inhibition of biofilm-related infections. Therefore, this review aims to describe the potential therapeutic strategies that can inhibit bacterial biofilm development; these include the usage of antiadhesion agents, AMPs, bacteriophages, QSIs, aptamers, NPs and PNAs, which can prevent or eradicate the formation of biofilms. These antibiofilm agents represent a promising therapeutic target in the treatment of biofilm infections and development of a strong capability to interfere with different phases of the biofilm development, including adherence, polysaccharide intercellular adhesion (PIA), quorum sensing molecules and cell-to-cell connection, bacterial aggregation, planktonic bacteria killing and host-immune response modulation. In addition, these components, in combination with antibiotics, can lead to the development of some kind of powerful combined therapy against bacterial biofilm-related infections.
Collapse
Affiliation(s)
- Fatemeh Hemmati
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Saba Ebrahimzadeh
- Department of Food Science and Technology, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
| | - Leila Yousefi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roghayeh Nouri
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
19
|
Pereira S, Yao R, Gomes M, Jørgensen PT, Wengel J, Azevedo NF, Sobral Santos R. Can Vitamin B12 Assist the Internalization of Antisense LNA Oligonucleotides into Bacteria? Antibiotics (Basel) 2021; 10:antibiotics10040379. [PMID: 33916701 PMCID: PMC8065541 DOI: 10.3390/antibiotics10040379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/18/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
The emergence of bacterial resistance to traditional small-molecule antibiotics is fueling the search for innovative strategies to treat infections. Inhibiting the expression of essential bacterial genes using antisense oligonucleotides (ASOs), particularly composed of nucleic acid mimics (NAMs), has emerged as a promising strategy. However, their efficiency depends on their association with vectors that can translocate the bacterial envelope. Vitamin B12 is among the largest molecules known to be taken up by bacteria and has very recently started to gain interest as a trojan-horse vector. Gapmers and steric blockers were evaluated as ASOs against Escherichia coli (E. coli). Both ASOs were successfully conjugated to B12 by copper-free azide-alkyne click-chemistry. The biological effect of the two conjugates was evaluated together with their intracellular localization in E. coli. Although not only B12 but also both B12-ASO conjugates interacted strongly with E. coli, they were mostly colocalized with the outer membrane. Only 6–9% were detected in the cytosol, which showed to be insufficient for bacterial growth inhibition. These results suggest that the internalization of B12-ASO conjugates is strongly affected by the low uptake rate of the B12 in E. coli and that further studies are needed before considering this strategy against biofilms in vivo.
Collapse
Affiliation(s)
- Sara Pereira
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Ruwei Yao
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Mariana Gomes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Per Trolle Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.Y.); (P.T.J.); (J.W.)
| | - Nuno Filipe Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
| | - Rita Sobral Santos
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, R. Dr. Roberto Frias, 4200-465 Porto, Portugal; (S.P.); (M.G.); (N.F.A.)
- Correspondence:
| |
Collapse
|
20
|
Yan Y, Li Y, Zhang Z, Wang X, Niu Y, Zhang S, Xu W, Ren C. Advances of peptides for antibacterial applications. Colloids Surf B Biointerfaces 2021; 202:111682. [PMID: 33714188 DOI: 10.1016/j.colsurfb.2021.111682] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/09/2020] [Accepted: 03/05/2021] [Indexed: 01/08/2023]
Abstract
In the past few decades, peptide antibacterial products with unique antibacterial mechanisms have attracted widespread interest. They can effectively reduce the probability of drug resistance of bacteria and are biocompatible, so they possess tremendous development prospects. This review provides recent research and analysis on the basic types of antimicrobial peptides (including poly (amino acid)s, short AMPs, and lipopeptides) and factors to optimize antimicrobial effects. It also summarizes the two most important modes of action of antimicrobial peptides and the latest developments in the application of AMPs, including antimicrobial agent, wound healing, preservative, antibacterial coating and others. Finally, we discuss the remaining challenges to improve the antibacterial peptides and propose prospects in the field.
Collapse
Affiliation(s)
- Yuhan Yan
- School of Chemistry and Materials Science, Ludong University, Yantai, 264025, China
| | - Yuanze Li
- School of Chemistry and Materials Science, Ludong University, Yantai, 264025, China
| | - Zhiwen Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai, 264025, China
| | - Xinhao Wang
- School of Chemistry and Materials Science, Ludong University, Yantai, 264025, China
| | - Yuzhong Niu
- School of Chemistry and Materials Science, Ludong University, Yantai, 264025, China
| | - Shaohua Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai, 264025, China.
| | - Wenlong Xu
- School of Chemistry and Materials Science, Ludong University, Yantai, 264025, China.
| | - Chunguang Ren
- Yantai Institute of Materia Medica, Yantai, 264000, China.
| |
Collapse
|
21
|
Ghosh S, Cotta KB, Hande AA, Fernandes M, Mehra S. PNA-mediated efflux inhibition as a therapeutic strategy towards overcoming drug resistance in Mycobacterium smegmatis. Microb Pathog 2021; 151:104737. [PMID: 33453316 DOI: 10.1016/j.micpath.2021.104737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 11/27/2022]
Abstract
The emergence of antibiotic-resistant strains of Mycobacterium tuberculosis and the decelerating development of new and effective antibiotics has impaired the treatment of tuberculosis (TB). Efflux pump inhibitors (EPIs) have the potential to improve the efficacy of existing anti-TB drugs although with toxicity limitations. Peptide nucleic acids (PNAs), oligonucleotide mimics, by virtue of their high nucleic acid binding specificity have the capability to overcome this drawback. We, therefore, investigated the efflux pump inhibitory properties of a PNA designed against an efflux pump of Mycobacterium smegmatis. LfrA, an efflux pump found in M. smegmatis, is majorly involved in conferring innate drug resistance to this strain and, therefore, was selected as a target for gene silencing via PNA. qRT-PCR and EtBr assays confirmed the EPI activity of the anti-lfrA PNA. On testing the effect of the anti-lfrA PNA on the bactericidal activity of a fluoroquinolone, norfloxacin, we observed that 5 μM of anti-lfrA PNA in combination with norfloxacin led to an enhanced killing of up to 2.5 log-fold against wild-type and a lab-generated multidrug resistant strain, exemplifying its potential in countering resistance. Improved efficacy was also observed against intra-macrophage mycobacteria, where the drug-PNA combination enhanced bacterial clearance by 1.3 log-fold. Further, no toxicity was observed with PNA concentrations up to 4 times higher than the efficacious anti-lfrA PNA concentration. Thus, PNA, as an adjuvant, presents a novel and viable approach to rejuvenate anti-TB therapeutics.
Collapse
Affiliation(s)
| | - Karishma Berta Cotta
- Centre for Research in Nanotechnology and Science, IIT Bombay, Powai, Mumbai, India
| | - Aniket A Hande
- Université de Pau et des Pays de l'Adour E2S UPPA, CNRS, IPREM, Pau, France
| | - Moneesha Fernandes
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune, India
| | - Sarika Mehra
- WRCB, IIT Bombay, Powai, Mumbai, Maharashtra, India; Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
| |
Collapse
|
22
|
Jain S, Kaur J, Prasad S, Roy I. Nucleic acid therapeutics: a focus on the development of aptamers. Expert Opin Drug Discov 2020; 16:255-274. [PMID: 32990095 DOI: 10.1080/17460441.2021.1829587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Aptamers provide exciting opportunities for the development of specific and targeted therapeutic approaches. AREAS COVERED In this review, the authors discuss different therapeutic options available with nucleic acids, including aptamers, focussing on similarities and differences between them. The authors concentrate on case studies with specific aptamers, which exemplify their distinct advantages. The reasons for failure, wherever available, are deliberated upon. Attempts to accelerate the in vitro selection process have been discussed. Challenges with aptamers in terms of their specificity and targeted delivery and strategies to overcome these are described. Examples of precise regulation of systemic half-life of aptamers using antidotes are discussed. EXPERT OPINION Despite their nontoxic nature, a variety of reasons limit the therapeutic potential of aptamers in the clinic. The analysis of adverse effects observed with the pegnivacogin/anivamersen pair has highlighted the need to screen for preexisting PEG antibodies in any clinical trial involving pegylated molecules. Surprisingly, and promisingly, the ability of nucleic acid therapeutics to breach the blood brain barrier seems achievable. The recognition of specific motifs, e.g. G-quadruplex in thrombin-binding aptamers, or a 'nucleation' zone while designing aptamer-antidote pairs, is likely to accelerate the discovery of therapeutically efficacious molecules.
Collapse
Affiliation(s)
- Swati Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Jaskirat Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Punjab, India
| |
Collapse
|
23
|
Han H, Wang Z, Li T, Teng D, Mao R, Hao Y, Yang N, Wang X, Wang J. Recent progress of bacterial FtsZ inhibitors with a focus on peptides. FEBS J 2020; 288:1091-1106. [PMID: 32681661 DOI: 10.1111/febs.15489] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/27/2020] [Accepted: 07/08/2020] [Indexed: 12/23/2022]
Abstract
In recent years, the rise of antibiotic resistance has become a primary health problem. With the emergence of bacterial resistance, the need to explore and develop novel antibacterial drugs has become increasingly urgent. Filamentous temperature-sensitive mutant Z (FtsZ), a crucial cell division protein of bacteria, has become a vital antibacterial target. FtsZ is a filamentous GTPase; it is highly conserved in bacteria and shares less than 20% sequence identity with the eukaryotic cytoskeleton protein tubulin, indicating that FtsZ-targeting antibacterial agents may have a low cytotoxicity toward eukaryotes. FtsZ can form a dynamic Z-ring in the center of the cell resulting in cell division. Furthermore, disturbance in the assembly of FtsZ may affect cellular dynamics and bacterial cell survival, making it a fascinating target for drug development. This review focuses on the recent discovery of FtsZ inhibitors, including peptides, natural products, and other synthetic small molecules, as well as their mechanism of action, which could facilitate the discovery of novel FtsZ-targeting clinical drugs in the future.
Collapse
Affiliation(s)
- Huihui Han
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zhenlong Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ting Li
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Da Teng
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ruoyu Mao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ya Hao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Na Yang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xiumin Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jianhua Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| |
Collapse
|
24
|
Gholizadeh P, Köse Ş, Dao S, Ganbarov K, Tanomand A, Dal T, Aghazadeh M, Ghotaslou R, Ahangarzadeh Rezaee M, Yousefi B, Samadi Kafil H. How CRISPR-Cas System Could Be Used to Combat Antimicrobial Resistance. Infect Drug Resist 2020; 13:1111-1121. [PMID: 32368102 PMCID: PMC7182461 DOI: 10.2147/idr.s247271] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/26/2022] Open
Abstract
Rapid emergence of antibiotic-resistant bacteria has made it harder for us to combat infectious diseases and to develop new antibiotics. The clustered regularly interspaced short palindromic repeats - CRISPR-associated (CRISPR-Cas) system, as a bacterial adaptive immune system, is recognized as one of the new strategies for controlling antibiotic-resistant strains. The programmable Cas nuclease of this system used against bacterial genomic sequences could be lethal or could help reduce resistance of bacteria to antibiotics. Therefore, this study aims to review using the CRISPR-Cas system to promote sensitizing bacteria to antibiotics. We envision that CRISPR-Cas approaches may open novel ways for the development of smart antibiotics, which could eliminate multidrug-resistant (MDR) pathogens and differentiate between beneficial and pathogenic microorganisms. These systems can be exploited to quantitatively and selectively eliminate individual bacterial strains based on a sequence-specific manner, creating opportunities in the treatment of MDR infections, the study of microbial consortia, and the control of industrial fermentation.
Collapse
Affiliation(s)
- Pourya Gholizadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Şükran Köse
- Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Tepecik Training and Research Hospital, İzmir, Turkey
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d’Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Khudaverdi Ganbarov
- Department of Microbiology, Baku State University, Baku, Republic of Azerbaijan
| | - Asghar Tanomand
- Department of Basic Sciences, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Tuba Dal
- Department of Clinical Microbiology, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Mohammad Aghazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
25
|
Swenson CS, Heemstra JM. Peptide nucleic acids harness dual information codes in a single molecule. Chem Commun (Camb) 2020; 56:1926-1935. [PMID: 32009137 DOI: 10.1039/c9cc09905k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nature encodes the information required for life in two fundamental biopolymers: nucleic acids and proteins. Peptide nucleic acid (PNA), a synthetic analog comprised of nucleobases arrayed along a pseudopeptide backbone, has the ability to combine the power of nucleic acids to encode information with the versatility of amino acids to encode structure and function. Historically, PNA has been perceived as a simple nucleic acid mimic having desirable properties such as high biostability and strong affinity for complementary nucleic acids. In this feature article, we aim to adjust this perception by highlighting the ability of PNA to act as a peptide mimic and showing the largely untapped potential to encode information in the amino acid sequence. First, we provide an introduction to PNA and discuss the use of conjugation to impart tunable properties to the biopolymer. Next, we describe the integration of functional groups directly into the PNA backbone to impart specific physical properties. Lastly, we highlight the use of these integrated amino acid side chains to encode peptide-like sequences in the PNA backbone, imparting novel activity and function and demonstrating the ability of PNA to simultaneously mimic both a peptide and a nucleic acid.
Collapse
Affiliation(s)
- Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
| | | |
Collapse
|
26
|
Antibacterial Peptide Nucleic Acids-Facts and Perspectives. Molecules 2020; 25:molecules25030559. [PMID: 32012929 PMCID: PMC7038079 DOI: 10.3390/molecules25030559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is an escalating, worldwide problem. Due to excessive use of antibiotics, multidrug-resistant bacteria have become a serious threat and a major global healthcare problem of the 21st century. This fact creates an urgent need for new and effective antimicrobials. The common strategies for antibiotic discovery are based on either modifying existing antibiotics or screening compound libraries, but these strategies have not been successful in recent decades. An alternative approach could be to use gene-specific oligonucleotides, such as peptide nucleic acid (PNA) oligomers, that can specifically target any single pathogen. This approach broadens the range of potential targets to any gene with a known sequence in any bacterium, and could significantly reduce the time required to discover new antimicrobials or their redesign, if resistance arises. We review the potential of PNA as an antibacterial molecule. First, we describe the physicochemical properties of PNA and modifications of the PNA backbone and nucleobases. Second, we review the carriers used to transport PNA to bacterial cells. Furthermore, we discuss the PNA targets in antibacterial studies focusing on antisense PNA targeting bacterial mRNA and rRNA.
Collapse
|