1
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Saha E, Khan A, Mallick AI, Mitra J. Purpose-built multicomponent supramolecular silver(I)-hydrogels as membrane-targeting broad-spectrum antibacterial agents against multidrug-resistant pathogens. J Mater Chem B 2024. [PMID: 39140272 DOI: 10.1039/d4tb01355g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Membrane-targeting compounds are of immense interest to counter complicated multi-drug resistant infections. However, the broad-spectrum effect of such compounds is often unmet due to the surges of antibiotic resistance among majority of Gram-negative bacteria compared to Gram-positive species. Though amphiphiles, synthetic mimics of antimicrobial peptides etc, have been extensively explored for their potential to perturb bacterial membranes, small molecule-based supramolecular hydrogels have remained unexplored. The design of supramolecular hydrogels can be tuned on-demand, catering to desired applications, including facile bacterial membrane perturbation. Considering the strong biocidal properties of Ag-based systems and the bacterial membrane-targeting potential of appended primary amine groups, we designed self-assembled multicomponent supramolecular Ag(I)-hydrogels with urea and DATr (3,5-diamino-1,2,4-triazole) as ligands, which are predisposed for hydrogen bonding and interacting with negatively charged bacterial membranes at physiological pH. The synthesized supramolecular Ag(I)-hydrogels exhibited almost similar antibacterial activity against both Gram-negative (Campylobacter jejuni; C. jejuni) and Gram-positive (Staphylococcus aureus; S. aureus) bacteria, with minimal inhibitory concentration (MIC) of ∼60 μg mL-1. Ag(I)-hydrogels facilitated the disruption of the negatively charged bacterial membrane due to electrostatic interaction and complementary hydrogen bonding facilitated by DATr and urea. Sustained intracellular ROS generation in the presence of Ag(I)-hydrogel further expedited cell lysis. We envisage that the multicomponent supramolecular Ag(I)-hydrogels studied herein can be employed in designing effective antibacterial coatings on a range of medical devices, including surgical instruments. Moreover, the present form of the hydrogels has the potential to improve the antibacterial functionality of conventional antimicrobials, thus revitalizing the effective targeting of hard-to-treat multi-drug-resistant (MDR) bacterial infections in a clinical set up.
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Affiliation(s)
- Ekata Saha
- Inorganic Materials & Catalysis (IMC) Division, CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar-364002, Gujarat, India.
- Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters, CSIR-HRDC Campus, Ghaziabad-201002, UP, India
| | - Afruja Khan
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal-741246, India.
| | - Amirul Islam Mallick
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal-741246, India.
| | - Joyee Mitra
- Inorganic Materials & Catalysis (IMC) Division, CSIR-Central Salt & Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar-364002, Gujarat, India.
- Academy of Scientific and Innovative Research (AcSIR), AcSIR Headquarters, CSIR-HRDC Campus, Ghaziabad-201002, UP, India
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2
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Stephani J, Gerhards L, Khairalla B, Solov’yov IA, Brand I. How do Antimicrobial Peptides Interact with the Outer Membrane of Gram-Negative Bacteria? Role of Lipopolysaccharides in Peptide Binding, Anchoring, and Penetration. ACS Infect Dis 2024; 10:763-778. [PMID: 38259029 PMCID: PMC10862549 DOI: 10.1021/acsinfecdis.3c00673] [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: 12/05/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Gram-negative bacteria possess a complex structural cell envelope that constitutes a barrier for antimicrobial peptides that neutralize the microbes by disrupting their cell membranes. Computational and experimental approaches were used to study a model outer membrane interaction with an antimicrobial peptide, melittin. The investigated membrane included di[3-deoxy-d-manno-octulosonyl]-lipid A (KLA) in the outer leaflet and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in the inner leaflet. Molecular dynamics simulations revealed that the positively charged helical C-terminus of melittin anchors rapidly into the hydrophilic headgroup region of KLA, while the flexible N-terminus makes contacts with the phosphate groups of KLA, supporting melittin penetration into the boundary between the hydrophilic and hydrophobic regions of the lipids. Electrochemical techniques confirmed the binding of melittin to the model membrane. To probe the peptide conformation and orientation during interaction with the membrane, polarization modulation infrared reflection absorption spectroscopy was used. The measurements revealed conformational changes in the peptide, accompanied by reorientation and translocation of the peptide at the membrane surface. The study suggests that melittin insertion into the outer membrane affects its permeability and capacitance but does not disturb the membrane's bilayer structure, indicating a distinct mechanism of the peptide action on the outer membrane of Gram-negative bacteria.
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Affiliation(s)
- Justus
C. Stephani
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Bishoy Khairalla
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
- Research
Center Neurosensory Science, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
- CeNaD—Center
for Nanoscale Dynamics, Carl von Ossietzky
University of Oldenburg, 26111 Oldenburg, Germany
| | - Izabella Brand
- Department
of Chemistry, Carl von Ossietzky University
of Oldenburg, 26111 Oldenburg, Germany
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3
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Kurnaz LB, Barman S, Yang X, Fisher C, Outten FW, Nagarkatti P, Nagarkatti M, Tang C. Facial amphiphilic naphthoic acid-derived antimicrobial polymers against multi-drug resistant gram-negative bacteria and biofilms. Biomaterials 2023; 301:122275. [PMID: 37619264 PMCID: PMC10530118 DOI: 10.1016/j.biomaterials.2023.122275] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/19/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Inspired by the facial amphiphilic nature and antimicrobial efficacy of many antimicrobial peptides, this work reported facial amphiphilic bicyclic naphthoic acid derivatives with different ratios of charges to rings that were installed onto side chains of poly(glycidyl methacrylate). Six quaternary ammonium-charged (QAC) polymers were prepared to investigate the structure-activity relationship. These QAC polymers displayed potent antibacterial activity against various multi-drug resistant (MDR) gram-negative pathogens such as Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. Polymers demonstrated low hemolysis and high antimicrobial selectivity. Additionally, they were able to eradicate established biofilms and kill metabolically inactive dormant cells. The membrane permeabilization and depolarization results indicated a mechanism of action through membrane disruption. Two lead polymers showed no resistance from MDR-P. aeruginosa and MDR-K. pneumoniae. These facial amphiphiles are potentially a new class of potent antimicrobial agents to tackle the antimicrobial resistance for both planktonic and biofilm-related infections.
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Affiliation(s)
- Leman Buzoglu Kurnaz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, United States
| | - Swagatam Barman
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, United States
| | - Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, SC, 29209, United States
| | - Claire Fisher
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, United States
| | - F Wayne Outten
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, United States
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, SC, 29209, United States
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, SC, 29209, United States
| | - Chuanbing Tang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, United States.
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4
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Le M, Huang W, Ma Z, Shi Z, Li Q, Lin C, Wang L, Jia YG. Facially Amphiphilic Skeleton-Derived Antibacterial Cationic Dendrimers. Biomacromolecules 2023; 24:269-282. [PMID: 36495302 DOI: 10.1021/acs.biomac.2c01128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It is urgent to develop biocompatible and high-efficiency antimicrobial agents since microbial infections have always posed serious challenges to human health. Herein, through the marriage of facially amphiphilic skeletons and cationic dendrimers, high-density positively charged dendrimers D-CA6-N+ (G2) and D-CA2-N+ (G1) were designed and synthesized using the "branch" of facially amphiphilic bile acids, followed by their modification with quaternary ammonium charges. Both dendrimers could self-assemble into nanostructured micelles in aqueous solution. D-CA6-N+ displays potent antibacterial activity against Staphylococcus aureus and Escherichia coli, with minimum inhibitory concentrations (MICs) as low as 7.50 and 7.79 μM, respectively, and has an evidently stronger antibacterial activity than D-CA2-N+. Moreover, D-CA6-N+ can kill S. aureus faster than E. coli. The facial amphiphilicity of the bile acid skeleton facilitates the selective destruction of bacterial membranes and endows dendrimers with negligible hemolysis and cytotoxicity even under a high concentration of 16× MIC. In vivo studies show that D-CA6-N+ is much more effective and safer than penicillin G in treating S. aureus infection and promoting wound healing, which suggests facially amphiphilic skeleton-derived cationic dendrimers can be a promising approach to effectively enhance antibacterial activity and biocompatibility of antibacterial agent, simultaneously.
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Affiliation(s)
- Mengqi Le
- School of Biomedical Science and Engineering, South China University of Technology, Guangzhou510006, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China
| | - Wen Huang
- School of Materials Science and Engineering, South China University of Technology, Guangzhou510641, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China
| | - Zunwei Ma
- School of Materials Science and Engineering, South China University of Technology, Guangzhou510641, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China
| | - Zhifeng Shi
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China
| | - Qingtao Li
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China
| | - Caihong Lin
- School of Materials Science and Engineering, South China University of Technology, Guangzhou510641, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China
| | - Lin Wang
- School of Materials Science and Engineering, South China University of Technology, Guangzhou510641, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China.,Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou510006, China.,Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou510006, China.,Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China
| | - Yong-Guang Jia
- School of Materials Science and Engineering, South China University of Technology, Guangzhou510641, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China.,Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou510006, China.,Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou510006, China.,Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou510006, China
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5
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Gupta S, Arora A, Saini V, Mehta D, Khan MZ, Mishra DK, Yavvari PS, Singh A, Gupta SK, Srivastava A, Kumar Y, Verma V, Nandicoori VK, Bajaj A. Hydrophobicity of Cholic Acid-Derived Amphiphiles Dictates the Antimicrobial Specificity. ACS Biomater Sci Eng 2022; 8:4996-5007. [DOI: 10.1021/acsbiomaterials.2c00924] [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)
- Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Cluster, Faridabad 121001, Haryana, India
| | - Amit Arora
- Department of Chemistry, Guru Jambheshwar University of Science & Technology, Hisar 125001, Haryana, India
| | - Varsha Saini
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Cluster, Faridabad 121001, Haryana, India
| | - Devashish Mehta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Cluster, Faridabad 121001, Haryana, India
| | - Mehak Zahoor Khan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak K. Mishra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Cluster, Faridabad 121001, Haryana, India
| | - Prabhu Srinivas Yavvari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Archana Singh
- Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sonu Kumar Gupta
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
| | - Aasheesh Srivastava
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
| | - Vikas Verma
- Department of Chemistry, Guru Jambheshwar University of Science & Technology, Hisar 125001, Haryana, India
| | - Vinay K. Nandicoori
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Cluster, Faridabad 121001, Haryana, India
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6
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Rasras AJ, El-Naggar M, Safwat NA, Al-Qawasmeh RA. Cholyl 1,3,4-oxadiazole hybrid compounds: design, synthesis and antimicrobial assessment. Beilstein J Org Chem 2022; 18:631-638. [PMID: 35706993 PMCID: PMC9174839 DOI: 10.3762/bjoc.18.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 01/18/2023] Open
Abstract
A new chemical library based on the hybridization of cholic acid with the heterocyclic moiety 1,3,4-oxadizole was synthesized, and tested for antimicrobial activity against Gram-positive, Gram-negative bacteria, and fungi. Among the synthesized compounds, the most potent derivatives against S. aureus were 4t, 4i, 4p, and 4c with MIC values between 31 and 70 µg/mL, while compound 4p was the most active one against Bacillus subtilis with a MIC value of 70 µg/mL. Interestingly, compounds 4a and 4u exerted selective activity against Gram-positive bacteria. The synthesized compounds showed good activity against A. fumigatus and C. albicans and compound 4v exhibited selective activity against fungi only.
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Affiliation(s)
- Anas J Rasras
- Faculty of Science, Department of Chemistry, Al-Balqa Applied University, PO Box 19117, Al-Salt, Jordan
| | - Mohamed El-Naggar
- College of Sciences, Department of Chemistry, University of Sharjah, Pure and Applied, Chemistry Research Group, PO Box 27272, Sharjah, United Arab Emirates
| | - Nesreen A Safwat
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Nasr City, Cairo, 11371, Egypt
| | - Raed A Al-Qawasmeh
- College of Sciences, Department of Chemistry, University of Sharjah, Pure and Applied, Chemistry Research Group, PO Box 27272, Sharjah, United Arab Emirates
- Department of Chemistry, The University of Jordan, Amman 11942, Jordan
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7
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N-methyl Benzimidazole Tethered Cholic Acid Amphiphiles Can Eradicate S. aureus-Mediated Biofilms and Wound Infections. Molecules 2022; 27:molecules27113501. [PMID: 35684439 PMCID: PMC9182351 DOI: 10.3390/molecules27113501] [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: 04/01/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 01/16/2023] Open
Abstract
Infections associated with Gram-positive bacteria like S. aureus pose a major threat as these bacteria can develop resistance and thereby limit the applications of antibiotics. Therefore, there is a need for new antibacterials to mitigate these infections. Bacterial membranes present an attractive therapeutic target as these membranes are anionic in nature and have a low chance of developing modifications in their physicochemical features. Antimicrobial peptides (AMPs) can disrupt the microbial membranes via electrostatic interactions, but the poor stability of AMPs halts their clinical translation. Here, we present the synthesis of eight N-methyl benzimidazole substituted cholic acid amphiphiles as antibacterial agents. We screened these novel heterocyclic cholic acid amphiphiles against different pathogens. Among the series, CABI-6 outperformed the other amphiphiles in terms of bactericidal activity against S. aureus. The membrane disruptive property of CABI-6 using a fluorescence-based assay has also been investigated, and it was inferred that CABI-6 can enhance the production of reactive oxygen species. We further demonstrated that CABI-6 can clear the pre-formed biofilms and can mitigate wound infection in murine models.
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8
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Pranantyo D, Zhang K, Si Z, Hou Z, Chan-Park MB. Smart Multifunctional Polymer Systems as Alternatives or Supplements of Antibiotics To Overcome Bacterial Resistance. Biomacromolecules 2022; 23:1873-1891. [PMID: 35471022 DOI: 10.1021/acs.biomac.1c01614] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In recent years, infectious diseases have again become a critical threat to global public health largely due to the challenges posed by antimicrobial resistance. Conventional antibiotics have played a crucial role in combating bacterial infections; however, their efficacy is significantly impaired by widespread drug resistance. Natural antimicrobial peptides (AMPs) and their polymeric mimics demonstrate great potential for killing bacteria with low propensity of resistance as they target the microbial membrane rather than a specific molecular target, but they are also toxic to the host eukaryotic cells. To minimize antibiotics systemic spread and the required dose that promote resistance and to advocate practical realization of the promising activity of AMPs and polymers, smart systems to target bacteria are highly sought after. This review presents bacterial recognition by various specific targeting molecules and the delivery systems of active components in supramolecules. Bacteria-induced activations of antimicrobial-based nanoformulations are also included. Recent advances in the bacteria targeting and delivery of synthetic antimicrobial agents may assist in developing new classes of highly selective antimicrobial systems which can improve bactericidal efficacy and greatly minimize the spread of bacterial resistance.
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9
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Asad M, Laurent AD. Exploring structural dynamics and optical properties of UnaG fluorescent protein upon N57 mutations. Phys Chem Chem Phys 2022; 24:3816-3825. [PMID: 35084408 DOI: 10.1039/d1cp04681k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UnaG is a new class of fluorescence protein in which an endogenous ligand, namely bilirubin (BLR), plays the role of chromophore. Upon photoexcitation, holoUnaG emits green light. A single mutation at residue 57 induces a decrease in the fluorescence quantum yield. To our knowledge, no atomic simulation at the atomic level has been carried out to date to explain this fluorescence decay in N57A and N57Q mutants. Herein molecular dynamics simulations were carried out on wild-type (WT) UnaG and both mutants to investigate the structural impact of the mutation on its global structure, on BLR and the absorption spectra. Our study reveals significant global changes upon mutation at the protein entrance (L3, H2, and, H3) governing a BLR modification. BLR in WT UnaG is rather rigid while when embedded into N57A or N57Q, dihedral angles between endo and exo vinyl moieties and between A and B rings at the entrance of UnaG are strongly modified along with the number of inter-/intramolecular interactions. The water molecules play an important role in the modification of the shape of the binding cavity. For the first time, we show that the structural modifications upon ligand mutations are tightly related to the key structural changes in the protein such as Loop3 (L3), β sheet 2 (B2), and β sheet 3 (B3) dynamics. The present work suggests that the quenching of the fluorescence properties of UnaG mutants is mainly a non-radiative process closely related to the BLR flexibility induced by global structural changes.
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Affiliation(s)
- Mohammad Asad
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France.
| | - Adèle D Laurent
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France.
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10
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Oyeka EE, Babahan I, Eboma B, Ifeanyieze KJ, Okpareke OC, Coban EP, Özmen A, Coban B, Aksel M, Özdemir N, Groutso T, Ayogu JI, Yildiz U, Dinçer Bilgin M, Halil Biyik H, Schrage BR, Ziegler CJ, Asegbeloyin JN. Biologically active acylthioureas and their Ni(II) and Cu(II) Complexes: Structural, spectroscopic, anti-proliferative, nucleolytic and antimicrobial studies. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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11
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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12
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Unlocking the bacterial membrane as a therapeutic target for next-generation antimicrobial amphiphiles. Mol Aspects Med 2021; 81:100999. [PMID: 34325929 DOI: 10.1016/j.mam.2021.100999] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/21/2021] [Accepted: 07/16/2021] [Indexed: 11/21/2022]
Abstract
Gram-positive bacteria like Enterococcus faecium and Staphylococcus aureus, and Gram-negative bacteria like Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Spp. are responsible for most of fatal bacterial infections. Bacteria present a handful of targets like ribosome, RNA polymerase, cell wall biosynthesis, and dihydrofolate reductase. Antibiotics targeting the protein synthesis like aminoglycosides and tetracyclines, inhibitors of RNA/DNA synthesis like fluoroquinolones, inhibitors of cell wall biosynthesis like glycopeptides and β-lactams, and membrane-targeting polymyxins and lipopeptides have shown very good success in combating the bacterial infections. Ability of the bacteria to develop drug resistance is a serious public health challenge as bacteria can develop antimicrobial resistance against newly introduced antibiotics that enhances the challenge for antibiotic drug discovery. Therefore, bacterial membranes present a suitable therapeutic target for development of antimicrobials as bacteria can find it difficult to develop resistance against membrane-targeting antimicrobials. In this review, we present the recent advances in engineering of membrane-targeting antimicrobial amphiphiles that can be effective alternatives to existing antibiotics in combating bacterial infections.
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13
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Lin C, Wang Y, Le M, Chen KF, Jia YG. Recent Progress in Bile Acid-Based Antimicrobials. Bioconjug Chem 2021; 32:395-410. [PMID: 33683873 DOI: 10.1021/acs.bioconjchem.0c00642] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With the emergence of drug-resistant bacteria and the formation of biofilms by bacteria and fungi, microbial infections gradually threaten global health. Natural antimicrobial peptides (AMPs) have low susceptibility for developing resistance due to the membrane targeted mechanism, but instability and high manufacturing cost limit their applications in clinic. Bile acids, a group of steroids in the human body, with high stability, biocompatibility, and inherent facial amphiphilic structure similar to the characteristics of AMPs, have been applied to the biological field, such as drug delivery systems, self-healing hydrogels, antimicrobials, and so on. In this review, we mainly focus on the different classes of bile acid-based antimicrobials in recent years. Various designs and methods for the preparation of unimolecular antimicrobials with bile acid skeletons are first introduced, including coupling of primary amine, quaternary ammonium, and amino acid units with bile acid skeletons. Some representative oligomeric antimicrobials, including dimers of bile acids, are summarized. Finally, macromolecular antimicrobials bearing some positive charges at the main chain or side chain and interaction mechanisms of these bile acid-based antimicrobials are discussed.
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Affiliation(s)
- Caihong Lin
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China.,Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou 510006, China
| | - Yushi Wang
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China.,Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou 510006, China
| | - Mengqi Le
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China.,Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou 510006, China
| | - Kai-Feng Chen
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China.,Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou 510006, China
| | - Yong-Guang Jia
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641, China.,National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China.,Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou 510006, China.,Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou 510006, China.,Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, China
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14
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Pal G, Mehta D, Singh S, Magal K, Gupta S, Jha G, Bajaj A, Ramu VS. Foliar Application or Seed Priming of Cholic Acid-Glycine Conjugates can Mitigate/Prevent the Rice Bacterial Leaf Blight Disease via Activating Plant Defense Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:746912. [PMID: 34630495 PMCID: PMC8497891 DOI: 10.3389/fpls.2021.746912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/25/2021] [Indexed: 05/06/2023]
Abstract
Xanthomonas Oryzae pv. oryzae (Xoo) causes bacterial blight and Rhizoctonia solani (R. solani) causes sheath blight in rice accounting for >75% of crop losses. Therefore, there is an urgent need to develop strategies for the mitigation of these pathogen infections. In this study, we report the antimicrobial efficacy of Cholic Acid-Glycine Conjugates (CAGCs) against Xoo and R. solani. We show that CAGC C6 is a broad-spectrum antimicrobial and is also able to degrade biofilms. The application of C6 did not hamper plant growth and showed minimal effect on the plant cell membranes. Exogenous application of C6 on pre-infection or post-infection of Xoo on rice susceptible genotype Taichung native (TN1) can mitigate the bacterial load and improve resistance through upregulation of plant defense genes. We further demonstrate that C6 can induce plant defense responses when seeds were primed with C6 CAGC. Therefore, this study demonstrates the potential of CAGCs as effective antimicrobials for crop protection that can be further explored for field applications.
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Affiliation(s)
- Garima Pal
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Devashish Mehta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Saurabh Singh
- Laboratory of Plant Microbe Interactions, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Kalai Magal
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Gopaljee Jha
- Laboratory of Plant Microbe Interactions, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
- *Correspondence: Avinash Bajaj
| | - Vemanna S. Ramu
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
- Vemanna S. Ramu
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15
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Paternò GM, Bondelli G, Sakai VG, Sesti V, Bertarelli C, Lanzani G. The Effect of an Intramembrane Light-Actuator on the Dynamics of Phospholipids in Model Membranes and Intact Cells. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11517-11527. [PMID: 32903010 DOI: 10.1021/acs.langmuir.0c01846] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The noncovalent intercalation of amphiphilic molecules in the lipid membrane can be exploited to modulate efficiently the physical status of the membrane. Such effects are largely employed in a range of applications, spanning from drug-delivery to therapeutics. In this context, we have very recently developed an intramembrane photo-actuator consisting of an amphiphilic azobenzene molecule, namely ZIAPIN2. The selective photo-isomerization occurring in the lipid bilayer induces a photo-triggered change in the membrane thickness and capacitance, eventually permitting to evoke light-induced neuronal firing both in vitro and in vivo. Here, we present a study on the dynamical perturbation in the lipid membrane caused by ZIAPIN2 and its vehicle solvent, dimethyl sulfoxide. Effects on the dynamics occurring in the picosecond time range and at the molecular level are probed using quasi-elastic neutron scattering. By coupling experiments carried out both on model membranes and intact cells, we found that DMSO leads to a general retardation of the dynamics within a more dynamically ordered landscape, a result that we attribute to the dehydration at the interface. On the other hand, ZIAPIN2 partitioning produces a general softening of the bilayer owing to its interaction with the lipids. These data are in agreement with our recent studies, which indicate that the efficacy of ZIAPIN2 in triggering cellular signalling stems from its ability to mechanically perturb the bilayer as a whole, by forming light-sensitive membrane spanning dimers.
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Affiliation(s)
- Giuseppe M Paternò
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Pascoli 10, 20133 Milano, Italy
| | - Gaia Bondelli
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Pascoli 10, 20133 Milano, Italy
| | - Victoria Garcia Sakai
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, U.K
| | - Valentina Sesti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica ″Giulio Natta″, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Chiara Bertarelli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica ″Giulio Natta″, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - Guglielmo Lanzani
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Pascoli 10, 20133 Milano, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
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16
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Singla P, Salunke DB. Recent advances in steroid amino acid conjugates: Old scaffolds with new dimensions. Eur J Med Chem 2020; 187:111909. [DOI: 10.1016/j.ejmech.2019.111909] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/13/2022]
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17
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Gong C, Hou C, Yao M, Ren J. New Discoveries in Hybrid Orbitals to Characterize Molecules and Predict Biomolecular Interactions. J Chem Inf Model 2020; 60:17-21. [PMID: 31851496 DOI: 10.1021/acs.jcim.9b01078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Taking hydrogen bonds as a basis to explore biomolecular properties and interactions, we constructed the lone-pair electron (LPE) index and a molecular orbital fingerprint based on molecular hybrid orbitals to represent the ability of molecules to form hydrogen bonds. Then, a computational model was constructed to predict molecular interactions. The LPE and orbital fingerprint could effectively predict the biological properties and bioactivities of molecules. This study revealed the significance of hybrid orbitals for understanding cell biochemistry.
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Affiliation(s)
- Congcong Gong
- School of Food Science and Technology , South China University of Technology , Guangzhou 510641 , Guangdong , China
| | - Chuanli Hou
- School of Food Science and Technology , South China University of Technology , Guangzhou 510641 , Guangdong , China
| | - Maojin Yao
- State Key Laboratory of Oncology In South China , SUN YAT-SEN University Cancer Center , Guangzhou 510641 , Guangdong , China
| | - Jiaoyan Ren
- School of Food Science and Technology , South China University of Technology , Guangzhou 510641 , Guangdong , China
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18
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Kumar S, Thakur J, Yadav K, Mitra M, Pal S, Ray A, Gupta S, Medatwal N, Gupta R, Mishra D, Rani P, Padhi S, Sharma P, Kapil A, Srivastava A, Priyakumar UD, Dasgupta U, Thukral L, Bajaj A. Cholic Acid-Derived Amphiphile which Combats Gram-Positive Bacteria-Mediated Infections via Disintegration of Lipid Clusters. ACS Biomater Sci Eng 2019; 5:4764-4775. [PMID: 33448819 DOI: 10.1021/acsbiomaterials.9b00706] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Inappropriate and uncontrolled use of antibiotics results in the emergence of antibiotic resistance, thereby threatening the present clinical regimens to treat infectious diseases. Therefore, new antimicrobial agents that can prevent bacteria from developing drug resistance are urgently needed. Selective disruption of bacterial membranes is the most effective strategy for combating microbial infections as accumulation of genetic mutations will not allow for the emergence of drug resistance against these antimicrobials. In this work, we tested cholic acid (CA) derived amphiphiles tethered with different alkyl chains for their ability to combat Gram-positive bacterial infections. In-depth biophysical and biomolecular simulation studies suggested that the amphiphile with a hexyl chain (6) executes more effective interactions with Gram-positive bacterial membranes as compared to other hydrophobic counterparts. Amphiphile 6 is effective against multidrug resistant Gram-positive bacterial strains as well and does not allow the adherence of S. aureus on amphiphile 6 coated catheters implanted in mice. Further, treatment of wound infections with amphiphile 6 clears the bacterial infections. Therefore, the current study presents strategic guidelines in design and development of CA-derived membrane-targeting antimicrobials for Gram-positive bacterial infections.
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Affiliation(s)
- Sandeep Kumar
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India.,Manipal Academy of Higher Education, Tiger Circle Road, Madhav Nagar, Manipal-576104, Karnataka, India
| | - Jyoti Thakur
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal Bypass Road, Bhauri, Bhopal-462066, Madhya Pradesh, India
| | - Kavita Yadav
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India.,Manipal Academy of Higher Education, Tiger Circle Road, Madhav Nagar, Manipal-576104, Karnataka, India
| | - Madhurima Mitra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India
| | - Sanjay Pal
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India.,Kalinga Institute of Industrial Technology, KIIT Road, Patia, Bhubaneswar-751024, Odisha, India
| | - Arjun Ray
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, Opp: Sukhdev Vihar Bus Depot, New Delhi-110025, India
| | - Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India
| | - Nihal Medatwal
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India
| | - Ragini Gupta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India
| | - Deepakkumar Mishra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India
| | - Parul Rani
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India
| | - Siladitya Padhi
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Professor CR Rao Road, Gachibowli, Hyderabad-500032, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Sri Aurobindo Marg, Ansari Nagar, New Delhi-110029, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, Sri Aurobindo Marg, Ansari Nagar, New Delhi-110029, India
| | - Aasheesh Srivastava
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal Bypass Road, Bhauri, Bhopal-462066, Madhya Pradesh, India
| | - U Deva Priyakumar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Professor CR Rao Road, Gachibowli, Hyderabad-500032, India
| | - Ujjaini Dasgupta
- Amity Institute of Integrative Sciences and Health, Amity University, Amity Education Valley Gurugram, Panchgaon, Manesar, Gurugram-122413, Haryana, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, Opp: Sukhdev Vihar Bus Depot, New Delhi-110025, India
| | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone Faridabad-Gurgaon Expressway, Faridabad-121001, Haryana, India
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19
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Nussinov R, Tsai CJ, Shehu A, Jang H. Computational Structural Biology: Successes, Future Directions, and Challenges. Molecules 2019; 24:molecules24030637. [PMID: 30759724 PMCID: PMC6384756 DOI: 10.3390/molecules24030637] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/05/2019] [Accepted: 02/10/2019] [Indexed: 02/06/2023] Open
Abstract
Computational biology has made powerful advances. Among these, trends in human health have been uncovered through heterogeneous 'big data' integration, and disease-associated genes were identified and classified. Along a different front, the dynamic organization of chromatin is being elucidated to gain insight into the fundamental question of genome regulation. Powerful conformational sampling methods have also been developed to yield a detailed molecular view of cellular processes. when combining these methods with the advancements in the modeling of supramolecular assemblies, including those at the membrane, we are finally able to get a glimpse into how cells' actions are regulated. Perhaps most intriguingly, a major thrust is on to decipher the mystery of how the brain is coded. Here, we aim to provide a broad, yet concise, sketch of modern aspects of computational biology, with a special focus on computational structural biology. We attempt to forecast the areas that computational structural biology will embrace in the future and the challenges that it may face. We skirt details, highlight successes, note failures, and map directions.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Amarda Shehu
- Departments of Computer Science, Department of Bioengineering, and School of Systems Biology, George Mason University, Fairfax, VA 22030, USA.
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
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