1
|
Draviana HT, Fitriannisa I, Khafid M, Krisnawati DI, Widodo, Lai CH, Fan YJ, Kuo TR. Size and charge effects of metal nanoclusters on antibacterial mechanisms. J Nanobiotechnology 2023; 21:428. [PMID: 37968705 PMCID: PMC10648733 DOI: 10.1186/s12951-023-02208-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023] Open
Abstract
Nanomaterials, specifically metal nanoclusters (NCs), are gaining attention as a promising class of antibacterial agents. Metal NCs exhibit antibacterial properties due to their ultrasmall size, extensive surface area, and well-controlled surface ligands. The antibacterial mechanisms of metal NCs are influenced by two primary factors: size and surface charge. In this review, we summarize the impacts of size and surface charge of metal NCs on the antibacterial mechanisms, their interactions with bacteria, and the factors that influence their antibacterial effects against both gram-negative and gram-positive bacteria. Additionally, we highlight the mechanisms that occur when NCs are negatively or positively charged, and provide examples of their applications as antibacterial agents. A better understanding of relationships between antibacterial activity and the properties of metal NCs will aid in the design and synthesis of nanomaterials for the development of effective antibacterial agents against bacterial infections. Based on the remarkable achievements in the design of metal NCs, this review also presents conclusions on current challenges and future perspectives of metal NCs for both fundamental investigations and practical antibacterial applications.
Collapse
Affiliation(s)
- Hanny Tika Draviana
- Graduate Institute of Nanomedicine and Medical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
- International PhD Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
| | - Istikhori Fitriannisa
- Graduate Institute of Nanomedicine and Medical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
- International PhD Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
| | - Muhamad Khafid
- Department of Nursing, Faculty of Nursing and Midwivery, Universitas Nahdlatul Ulama Surabaya, Surabaya, 60237, East Java, Indonesia
| | - Dyah Ika Krisnawati
- Dharma Husada Nursing Academy, Kediri, 64117, East Java, Indonesia
- Department of Health Analyst, Faculty of Health, Universitas Nahdlatul Ulama Surabaya, Surabaya, 60237, East Java, Indonesia
| | - Widodo
- Sekolah Tinggi Teknologi Pomosda, Nganjuk, 64483, East Java, Indonesia
| | - Chien-Hung Lai
- Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 11031, Taiwan.
- Department of Physical Medicine and Rehabilitation, Taipei Medical University Hospital, Taipei, 11031, Taiwan.
- Taipei Neuroscience Institute, Taipei Medical University, Taipei, 11031, Taiwan.
| | - Yu-Jui Fan
- International PhD Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan.
- School of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan.
- Center for Precision Health and Quantitative Sciences, Taipei Medical University Hospital, Taipei, 11031, Taiwan.
| | - Tsung-Rong Kuo
- Graduate Institute of Nanomedicine and Medical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan.
- International PhD Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan.
- Precision Medicine and Translational Cancer Research Center, Taipei Medical University Hospital, Taipei, 11031, Taiwan.
- Stanford Byers Center for Biodesign, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
2
|
Cho THS, Pick K, Raivio TL. Bacterial envelope stress responses: Essential adaptors and attractive targets. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119387. [PMID: 36336206 DOI: 10.1016/j.bbamcr.2022.119387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/05/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
Millions of deaths a year across the globe are linked to antimicrobial resistant infections. The need to develop new treatments and repurpose of existing antibiotics grows more pressing as the growing antimicrobial resistance pandemic advances. In this review article, we propose that envelope stress responses, the signaling pathways bacteria use to recognize and adapt to damage to the most vulnerable outer compartments of the microbial cell, are attractive targets. Envelope stress responses (ESRs) support colonization and infection by responding to a plethora of toxic envelope stresses encountered throughout the body; they have been co-opted into virulence networks where they work like global positioning systems to coordinate adhesion, invasion, microbial warfare, and biofilm formation. We highlight progress in the development of therapeutic strategies that target ESR signaling proteins and adaptive networks and posit that further characterization of the molecular mechanisms governing these essential niche adaptation machineries will be important for sparking new therapeutic approaches aimed at short-circuiting bacterial adaptation.
Collapse
Affiliation(s)
- Timothy H S Cho
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Kat Pick
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tracy L Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
3
|
Pant P, Pathak A, Jayaram B. Symmetric Nucleosides as Potent Purine Nucleoside Phosphorylase Inhibitors. J Phys Chem B 2021; 125:2856-2862. [PMID: 33715357 DOI: 10.1021/acs.jpcb.0c10553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nucleic acids are one of the most enigmatic biomolecules crucial to several biological processes. Nucleic acid-protein interactions are vital for the coordinated and controlled functioning of a cell, leading to the design of several nucleoside/nucleotide analogues capable of mimicking these interactions and hold paramount importance in the field of drug discovery. Purine nucleoside phosphorylase is a well-established drug target due to its association with numerous immunodeficiency diseases. Here, we study the binding of human purine nucleoside phosphorylase (PNP) to some bidirectional symmetric nucleosides, a class of nucleoside analogues that are more flexible due to the absence of sugar pucker restraints. We compared the binding energies of PNP-symmetric nucleosides to the binding energies of PNP-inosine/Imm-H (a transition-state analogue), by means of 200 ns long all-atom explicit-solvent Gaussian accelerated molecular dynamics simulations followed by energetics estimation using the MM-PBSA methodology. Quite interestingly, we observed that a few symmetric nucleosides, namely, ν3 and ν4, showed strong binding with PNP (-14.1 and -12.6 kcal/mol, respectively), higher than inosine (-6.3 kcal/mol) and Imm-H (-9.6 kcal/mol). This is rationalized by an enhanced hydrogen-bond network for symmetric nucleosides compared to inosine and Imm-H while maintaining similar van der Waals contacts. We note that the chemical structures of both ν3 and ν4, due to an additional unsaturation in them, resemble enzymatic transition states and fall in the category of transition-state analogues (TSAs), which are quite popular.
Collapse
Affiliation(s)
- Pradeep Pant
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi 110016, India
| | - Amita Pathak
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi 110016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi 110016, India.,Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| |
Collapse
|
5
|
Pant P, Jayaram B. C5' omitted DNA enhances bendability and protein binding. Biochem Biophys Res Commun 2019; 514:979-984. [PMID: 31092333 DOI: 10.1016/j.bbrc.2019.05.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 12/24/2022]
Abstract
Protein-DNA interactions are of great biological importance. The specificity and strength of these intimate contacts are crucial in the proper functioning of a cell, wherein the role of DNA dynamic bendability has been a matter of discussion. We relate DNA bendability to protein binding by introducing some simple modifications in the DNA structure. We removed C5' carbon in first modified structure and the second has an additional carbon between C3' and 3'-OH, hereby pronounced as C(-) and C(+) nucleic acids respectively. We observed that C(+) nucleic acid retains B-DNA duplex as seen by means of 500 ns long molecular dynamics (MD) simulations, structural and energetic calculations, while C(-) nucleic acid attains a highly bend structure. We transferred these observations to a protein-DNA system in order to monitor as to what extent the bendability enhances the protein binding. The energetics of binding is explored by performing 100 ns long MD simulations on control and modified DNA-protein complexes followed by running MM-PBSA/GBSA calculations on the resultant structures. It is observed that C(+) nucleic acid has protein binding in close correspondence to the control system (∼-14 kcal/mol) due to their relatable structure, while the C(-) nucleic acid displayed high binding to the protein (∼-18 kcal/mol). DelPhi based calculations reveal that the high binding could be the result of enhanced electrostatic interactions caused by exposed bases in the bend structure for protein recognition. Such modified oligonucleotides, due to their improved binding to protein and resistance to nuclease degradation, have a great therapeutic value.
Collapse
Affiliation(s)
- Pradeep Pant
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, 110016, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India; Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, 110016, India; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
| |
Collapse
|
6
|
Tsai KC, Hung PP, Cheng CF, Chen C, Tseng TS. Exploring the mode of action of inhibitors targeting the PhoP response regulator of Salmonella enterica through comprehensive pharmacophore approaches. RSC Adv 2019; 9:9308-9312. [PMID: 35517705 PMCID: PMC9062048 DOI: 10.1039/c9ra00620f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/28/2019] [Indexed: 11/23/2022] Open
Abstract
The PhoQ/PhoP two-component system regulates the physiological and virulence functions of Salmonella enterica. However, the mode of action of known PhoP inhibitors is unclear. We systematically constructed a pharmacophore model of inhibitors to probe the interface pharmacophore model of the PhoP dimer, coupling it with Ligplot analysis. We found that these inhibitors bind on the α5-helix, altering the conformation and interfering with PhoP binding on DNA. Comprehensive pharmacophore approaches explore the mode of action of inhibitors targeting PhoP response regulator of Salmonella enterica.![]()
Collapse
Affiliation(s)
- Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare Taipei 112 Taiwan.,The PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University Taipei Taiwan
| | - Po-Pin Hung
- Division of Infectious Disease, Department of Internal Medicine, Taipei Tzu Chi Hospital, The Buddhist Tzu Chi Medical Foundation New Taipei City 231 Taiwan
| | - Ching-Feng Cheng
- Department of Pediatrics, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taipei and Tzu Chi University Hualien Taiwan.,Institute of Biomedical Sciences, Academia Sinica Taipei 115 Taiwan
| | - Chinpan Chen
- Institute of Biomedical Sciences, Academia Sinica Taipei 115 Taiwan
| | - Tien-Sheng Tseng
- Department of Research, Taipei Tzu Chi Hospital, The Buddhist Tzu Chi Medical Foundation New Taipei City 231 Taiwan
| |
Collapse
|