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Pfukwa NBC, Rautenbach M, Hunt NT, Olaoye OO, Kumar V, Parker AW, Minnes L, Neethling PH. Temperature-Induced Effects on the Structure of Gramicidin S. J Phys Chem B 2023; 127:3774-3786. [PMID: 37125750 DOI: 10.1021/acs.jpcb.2c06115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We report on the structure of Gramicidin S (GS) in a model membrane mimetic environment represented by the amphipathic solvent 1-octanol using one-dimensional (1D) and two-dimensional (2D) IR spectroscopy. To explore potential structural changes of GS, we also performed a series of spectroscopic measurements at differing temperatures. By analyzing the amide I band and using 2D-IR spectral changes, results could be associated to the disruption of aggregates/oligomers, as well as structural and conformational changes happening in the concentrated solution of GS. The ability of 2D-IR to enable differentiation in melting transitions of oligomerized GS structures is attributed to the sensitivity of the technique to vibrational coupling. Two melting transition temperatures were identified; at Tm1 in the range 41-47 °C where the GS aggregates/oligomers disassemble and at Tm2 = 57 ± 2 °C where there is significant change involving GS β-sheet-type hydrogen bonds, whereby it is proposed that there is loss of interpeptide hydrogen bonds and we are left with mainly intrapeptide β-sheet and β-turn hydrogen bonds of the smaller oligomers. Further analysis with quantum mechanical/molecular mechanics (QM/MM) simulations and second derivative results highlighted the participation of active GS side chains. Ultimately, this work contributes toward understanding the GS structure and the formulation of GS analogues with improved bioactivity.
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Affiliation(s)
- Ngaatendwe B C Pfukwa
- Department of Physics, Laser Research Institute, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Marina Rautenbach
- BIOPEP Peptide Group, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Olufemi O Olaoye
- Department of Physics, Laser Research Institute, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Vikas Kumar
- BIOPEP Peptide Group, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Anthony W Parker
- Department of Physics, Laser Research Institute, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- Research Complex at Harwell, Rutherford Appleton Laboratory, STFC Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Lucy Minnes
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Pieter H Neethling
- Department of Physics, Laser Research Institute, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Design, characterization and structure-function analysis of novel antimicrobial peptides based on the N-terminal CATH-2 fragment. Sci Rep 2022; 12:12058. [PMID: 35835842 PMCID: PMC9283491 DOI: 10.1038/s41598-022-16303-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/07/2022] [Indexed: 11/28/2022] Open
Abstract
The emergence of multidrug resistance coupled with shrinking antibiotic pipelines has increased the demand of antimicrobials with novel mechanisms of action. Therefore, researchers across the globe are striving to develop new antimicrobial substances to alleviate the pressure on conventional antibiotic therapies. Host-Defence Peptides (HDPs) and their derivatives are emerging as effective therapeutic agents against microbial resistance. In this study, five analogs (DP1-5) of the N-terminal (N-15) fragment of CATH-2 were designed based on the delicate balance between various physicochemical properties such as charge, aliphatic character, amphipathicity and hydrophobicity. By means of in-silico and in-vitro studies a novel peptide (DP1) with the sequence “RFGRFLRKILRFLKK” was found to be more effective and less toxic than the N-terminal CATH-2 peptide. Circular dichroism spectroscopy and differential scanning calorimetry were applied for structural insights. Antimicrobial, haemolytic, and cytotoxic activities were also assessed. The resulting peptide was characterized by low cytotoxicity, low haemolytic activity, and efficient anti-microbial activity. Structurally, it displayed strong helical properties irrespective of the solvent environment and was stable in membrane-mimicking environments. Taken together, the data suggests that DP1 can be explored as a promising therapeutic agent with possible clinical applications.
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Wei DX, Zhang XW. Biosynthesis, Bioactivity, Biosafety and Applications of Antimicrobial Peptides for Human Health. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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4
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Antezana PE, Municoy S, Bellino MG, Martini MF, Desimone MF. Nanodelivery of the Gramicidin Peptide for Enhancing Antimicrobial Activity. EUR J LIPID SCI TECH 2021. [DOI: 10.1002/ejlt.202000389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Pablo E. Antezana
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Metabolismo del Fármaco (IQUIMEFA) Facultad de Farmacia y Bioquímica Junín 956, (1113) Buenos Aires Argentina
| | - Sofia Municoy
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Metabolismo del Fármaco (IQUIMEFA) Facultad de Farmacia y Bioquímica Junín 956, (1113) Buenos Aires Argentina
| | - Martín G. Bellino
- Instituto de Nanociencia y Nanotecnología – Comisión Nacional de Energía Atómica y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Av. General Paz 1499, (1650) San Martín Argentina
| | - M. Florencia Martini
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Metabolismo del Fármaco (IQUIMEFA) Facultad de Farmacia y Bioquímica Junín 956, (1113) Buenos Aires Argentina
| | - Martín F. Desimone
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Química y Metabolismo del Fármaco (IQUIMEFA) Facultad de Farmacia y Bioquímica Junín 956, (1113) Buenos Aires Argentina
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PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach. BIOTECH 2021; 10:biotech10020008. [PMID: 35822818 PMCID: PMC9245465 DOI: 10.3390/biotech10020008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/30/2022] Open
Abstract
Fusarium oxysporum remains one of the leading causes of economic losses and poor crop yields; its detection is strained due to its presentation in various morphological and physiological forms. This research work sought to identify novel biomarkers for the detection of Fusarium oxysporum using in silico approaches. Experimentally validated anti-Fusarium oxysporum antimicrobial peptides (AMPs) were used to construct a profile against Fusarium oxysporum. The performance and physicochemical parameters of these peptides were predicted. The gene for the Fusarium oxysporum receptor protein PR-1-like Protein, Fpr1, was identified and translated. The resulting protein model from the translation was then validated. The anti-Fusarium oxysporum AMPs and Fusarium oxysporum receptor protein 3-D structures were characterized, and their docking interaction analyses were carried out. The HMMER in silico tool identified novel anti-Fusarium oxysporum antimicrobial peptides with good performance in terms of accuracy, sensitivity, and specificity. These AMPs also displayed good physicochemical properties and bound with greater affinity to Fusarium oxysporum protein receptor PR-1-like Protein. The tendency of these AMPs to precisely detect Fusarium oxysporum PR-1-like Protein, Fpr1, would justify their use for the identification of the fungus. This study would enhance and facilitate the identification of Fusarium oxysporum to reduce problems associated with poor crop yield, economic losses, and decreased nutritional values of plants to keep up with the growing population.
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Bakare OO, Keyster M, Pretorius A. Identification of biomarkers for the accurate and sensitive diagnosis of three bacterial pneumonia pathogens using in silico approaches. BMC Mol Cell Biol 2020; 21:82. [PMID: 33218302 PMCID: PMC7678116 DOI: 10.1186/s12860-020-00328-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/09/2020] [Indexed: 11/10/2022] Open
Abstract
Background Pneumonia ranks as one of the main infectious sources of mortality among kids under 5 years of age, killing 2500 a day; late research has additionally demonstrated that mortality is higher in the elderly. A few biomarkers, which up to this point have been distinguished for its determination lack specificity, as these biomarkers fail to build up a differentiation between pneumonia and other related diseases, for example, pulmonary tuberculosis and Human Immunodeficiency Infection (HIV). There is an inclusive global consensus of an improved comprehension of the utilization of new biomarkers, which are delivered in light of pneumonia infection for precision identification to defeat these previously mentioned constraints. Antimicrobial peptides (AMPs) have been demonstrated to be promising remedial specialists against numerous illnesses. This research work sought to identify AMPs as biomarkers for three bacterial pneumonia pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Acinetobacter baumannii using in silico technology. Hidden Markov Models (HMMER) was used to identify putative anti-bacterial pneumonia AMPs against the identified receptor proteins of Streptococcus pneumoniae, Klebsiella pneumoniae, and Acinetobacter baumannii. The physicochemical parameters of these putative AMPs were computed and their 3-D structures were predicted using I-TASSER. These AMPs were subsequently subjected to docking interaction analysis against the identified bacterial pneumonia pathogen proteins using PATCHDOCK. Results The in silico results showed 18 antibacterial AMPs which were ranked based on their E values with significant physicochemical parameters in conformity with known experimentally validated AMPs. The AMPs also bound the pneumonia receptors of their respective pathogens sensitively at the extracellular regions. Conclusions The propensity of these AMPs to bind pneumonia pathogens proteins justifies that they would be potential applicant biomarkers for the recognizable detection of these bacterial pathogens in a point-of-care POC pneumonia diagnostics. The high sensitivity, accuracy, and specificity of the AMPs likewise justify the utilization of HMMER in the design and discovery of AMPs for disease diagnostics and therapeutics.
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Affiliation(s)
- Olalekan Olanrewaju Bakare
- Bioinformatics Research Group, Biotechnology Department, University of the Western Cape, Cape Town, 7535, South Africa. .,Environmental Biotechnology Laboratory, Biotechnology Department, University of the Western Cape, Cape Town, 7535, South Africa.
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Biotechnology Department, University of the Western Cape, Cape Town, 7535, South Africa
| | - Ashley Pretorius
- Bioinformatics Research Group, Biotechnology Department, University of the Western Cape, Cape Town, 7535, South Africa
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7
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Ghosh U, Soni I, Kaul G, Trivedi P, Chaturvedi V, Chopra S, Kanti Chakraborty T. Synthesis and Biological Studies of Dodecameric Cationic Antimicrobial Peptides Containing Tetrahydrofuran Amino Acids. Chembiochem 2020; 21:2518-2526. [PMID: 32297461 DOI: 10.1002/cbic.202000163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/13/2020] [Indexed: 11/05/2022]
Abstract
We report here a concise route to synthesize various stereoisomers of tetrahydrofuran amino acids (TAAs) and the synthesis of TAA-containing linear cationic dodecapeptides. Some of these linear peptides show slightly better antimicrobial activities than their tetra- and octameric congeners, but no activity against Mycobacterium tuberculosis, for which octapeptides exhibited by far the best results; this implies that antibacterial activity is dependent on the length of these linear peptides. All the dodecapeptides described here were found to be toxic in nature against Vero cells. The study helps to delineate the optimal length of this series of linear peptides and select potential leads in the development of novel cationic peptide-based antibiotics.
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Affiliation(s)
- Uttam Ghosh
- Department of Organic Chemistry, Indian Institution of Science, Bengaluru, 560012, Karnataka, India
| | - Isha Soni
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Grace Kaul
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Priyanka Trivedi
- Division of Biochemistry, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Vinita Chaturvedi
- Division of Biochemistry, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Tushar Kanti Chakraborty
- Department of Organic Chemistry, Indian Institution of Science, Bengaluru, 560012, Karnataka, India
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8
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Aragón-Muriel A, Ausili A, Sánchez K, Rojas A OE, Londoño Mosquera J, Polo-Cerón D, Oñate-Garzón J. Studies on the Interaction of Alyteserin 1c Peptide and Its Cationic Analogue with Model Membranes Imitating Mammalian and Bacterial Membranes. Biomolecules 2019; 9:biom9100527. [PMID: 31557903 PMCID: PMC6843542 DOI: 10.3390/biom9100527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 01/17/2023] Open
Abstract
Antimicrobial peptides (AMPs) are effector molecules of the innate immune system and have been isolated from multiple organisms. Their antimicrobial properties are due to the fact that they interact mainly with the anionic membrane of the microorganisms, permeabilizing it and releasing the cytoplasmic content. Alyteserin 1c (+2), an AMP isolated from Alytes obstetricans and its more cationic and hydrophilic analogue (+5) were synthesized using the solid phase method, in order to study the interaction with model membranes by calorimetric and spectroscopic assays. Differential scanning calorimetry (DSC) showed that both peptides had a strong effect when the membrane contained phosphatidylcholine (PC) alone or was mixed with phosphatidylglycerol (PG), increasing membrane fluidization. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was used to study the secondary structure of the peptide. Peptide +2 exhibited a transition from β-sheet/turns to β-sheet/α-helix structures after binding with model membranes, whereas peptide +5 had a transition from aggregation/unordered to β-sheet/α-helix structures after binding with membrane-contained PC. Interestingly, the latter showed a β-sheet structure predominantly in the presence of PG lipids. Additionally, molecular dynamics (MD) results showed that the carboxy-terminal of the peptide +5 has the ability to insert into the surface of the PC/PG membranes, resulting in the increase of the membrane fluidity.
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Affiliation(s)
- Alberto Aragón-Muriel
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Alessio Ausili
- Departmento de Bioquímica y Biología Molecular-A, Facultad de Medicina Veterinaria, Campus of International Excellence Mare, Universidad de Murcia, E-30100 Murcia, Spain.
| | - Kevin Sánchez
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
| | - Oscar E Rojas A
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
| | - Juan Londoño Mosquera
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Dorian Polo-Cerón
- Facultad de Ciencias Naturales y Exactas, Departmento de Química, Laboratorio of Investigación en Catalisis and Procesos (LICAP), Universidad del Valle, Cali 760001, Colombia.
| | - Jose Oñate-Garzón
- Grupo de Investigación en Química y Biotecnología (QUIBIO), Facultad de Ciencias Básicas, Universidad Santiago de Cali, Cali 760031, Colombia.
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9
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Repurposing the scorpion venom peptide VmCT1 into an active peptide against Gram-negative ESKAPE pathogens. Bioorg Chem 2019; 90:103038. [DOI: 10.1016/j.bioorg.2019.103038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/28/2019] [Accepted: 06/03/2019] [Indexed: 01/24/2023]
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10
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Blanco MJ. Building upon Nature's Framework: Overview of Key Strategies Toward Increasing Drug-Like Properties of Natural Product Cyclopeptides and Macrocycles. Methods Mol Biol 2019; 2001:203-233. [PMID: 31134573 DOI: 10.1007/978-1-4939-9504-2_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The pharmaceutical industry has focused mainly in the development of small-molecule entities intended for oral administration for the past decades. As a result, the majority of existing drugs address only a narrow range of biological targets. In the era of post-genomics, transcriptomics, and proteomics, there is an increasing interest on larger modulators of proteins that can span larger surfaces, access new therapeutic mechanisms of action, and provide greater target specificity. Traditional drug-like molecules developed using "rule-of-five" (Ro5) guidelines have been proven ineffective against a variety of challenging targets, such as protein-protein interactions, nucleic acid complexes, and antibacterial modalities. However, natural products are known to be effective at modulating such targets, leading to a renewed focus by medicinal chemists on investigating underrepresented chemical scaffolds associated with natural products. Here we describe recent efforts toward identification of novel natural cyclopeptides and macrocycles as well as selected medicinal chemistry strategies to increase drug-like properties or further exploration of their activity.
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The Multifaceted Antibacterial Mechanisms of the Pioneering Peptide Antibiotics Tyrocidine and Gramicidin S. mBio 2018; 9:mBio.00802-18. [PMID: 30301848 PMCID: PMC6178620 DOI: 10.1128/mbio.00802-18] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Cyclic β-sheet decapeptides, such as tyrocidines and gramicidin S, were among the first antibiotics in clinical application. Although they have been used for such a long time, there is virtually no resistance to them, which has led to a renewed interest in this peptide class. Both tyrocidines and gramicidin S are thought to disrupt the bacterial membrane. However, this knowledge is mainly derived from in vitro studies, and there is surprisingly little knowledge about how these long-established antibiotics kill bacteria. Our results shed new light on the antibacterial mechanism of β-sheet peptide antibiotics and explain why they are still so effective and why there is so little resistance to them. Cyclic β-sheet decapeptides from the tyrocidine group and the homologous gramicidin S were the first commercially used antibiotics, yet it remains unclear exactly how they kill bacteria. We investigated their mode of action using a bacterial cytological profiling approach. Tyrocidines form defined ion-conducting pores, induce lipid phase separation, and strongly reduce membrane fluidity, resulting in delocalization of a broad range of peripheral and integral membrane proteins. Interestingly, they also cause DNA damage and interfere with DNA-binding proteins. Despite sharing 50% sequence identity with tyrocidines, gramicidin S causes only mild lipid demixing with minor effects on membrane fluidity and permeability. Gramicidin S delocalizes peripheral membrane proteins involved in cell division and cell envelope synthesis but does not affect integral membrane proteins or DNA. Our results shed a new light on the multifaceted antibacterial mechanisms of these antibiotics and explain why resistance to them is virtually nonexistent.
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12
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Wan Y, Stanovych A, Gori D, Zirah S, Kouklovsky C, Alezra V. β,γ-diamino acids as building blocks for new analogues of Gramicidin S: Synthesis and biological activity. Eur J Med Chem 2018; 149:122-128. [DOI: 10.1016/j.ejmech.2018.02.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/05/2018] [Accepted: 02/16/2018] [Indexed: 01/15/2023]
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13
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Singh G, Azmi S, Ghosh JK, Ampapathi RS, Pal S. Synthesis and Conformational Studies of Taa-Containingo-Nitrobenzenesulfonamide- (o-Nosyl-) Protected GS Analogs to Prove the Importance of 6RStereochemistry of Taa over 6S. ChemistrySelect 2018. [DOI: 10.1002/slct.201800003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Gajendra Singh
- NMR Research Centre; Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Sarfuddin Azmi
- Molecular and Structural Biology Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Present Address: Research Centre; Prince Sultan Military Medical City, Riyadh, Kingdom of; Saudi Arabia
| | - Jimut Kanti Ghosh
- Molecular and Structural Biology Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Ravi Sankar Ampapathi
- NMR Research Centre; Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Sudip Pal
- Medicinal & Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Department of Chemistry, School of Physical Sciences; Sikkim University (A Central University); Gangtok 737102 India
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14
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Affiliation(s)
- Garry Laverty
- Biofunctional Nanomaterials Group, School of Pharmacy, Queen's University Belfast, Belfast, Co Antrim BT9 7BL, Northern Ireland
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15
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Priem C, Wuttke A, Berditsch M, Ulrich AS, Geyer A. Scaling the Amphiphilic Character and Antimicrobial Activity of Gramicidin S by Dihydroxylation or Ketal Formation. J Org Chem 2017; 82:12366-12376. [DOI: 10.1021/acs.joc.7b02177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Priem
- Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - André Wuttke
- Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Marina Berditsch
- Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Anne S. Ulrich
- Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Armin Geyer
- Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
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16
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The increase in positively charged residues in cecropin D-like Galleria mellonella favors its interaction with membrane models that imitate bacterial membranes. Arch Biochem Biophys 2017; 629:54-62. [DOI: 10.1016/j.abb.2017.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/16/2017] [Accepted: 07/13/2017] [Indexed: 01/30/2023]
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17
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Liu B, Zhang W, Gou S, Huang H, Yao J, Yang Z, Liu H, Zhong C, Liu B, Ni J, Wang R. Intramolecular cyclization of the antimicrobial peptide Polybia-MPI with triazole stapling: influence on stability and bioactivity. J Pept Sci 2017; 23:824-832. [PMID: 28833783 DOI: 10.1002/psc.3031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/14/2017] [Accepted: 07/17/2017] [Indexed: 12/23/2022]
Abstract
Cationic antimicrobial peptides have attracted increasing attention as a novel class of antibiotics to treat infectious diseases caused by pathogenic bacteria. However, susceptibility to protease is a shortcoming in their development. Cyclization is one approach to increase the proteolytic resistance of peptides. Therefore, to improve the proteolytic resistance of Polybia-MPI, we have synthesized the MPI cyclic analogs C-MPI-1 (i-to-i+4) and C-MPI-2 (i-to-i+6) by copper(I)-catalyzed azide-alkyne cycloaddition. Compared with MPI, C-MPI-1 displayed sustained antimicrobial activity and had enhanced anti-trypsin resistance, while C-MPI-2 displayed no antimicrobial activity. The relationship between peptide structure and bioactivity was further investigated by probing the secondary structure of the peptides by circular dichroism. This showed that C-MPI-1 adopted an α-helical structure in aqueous solution and, interestingly, had increased α-helical conformation in 30 mM sodium dodecyl sulfate and 50% trifluoroethyl alcohol compared with MPI. C-MPI-2 that was not α-helical in structure, suggesting that the propensity for α-helix conformation may play an important role in cyclic peptide design. In addition, scanning electron microscopy, propidium iodide uptake, and membrane permeabilization assays indicated that MPI and the optimized analog C-MPI-1 had membrane-active action modes, indicating that the peptides would not be susceptible to conventional resistance mechanisms. Our study provides additional insight into the influence of intramolecular cyclization at various positions on peptide structure and biological activity. In conclusion, the design and synthesis of cyclic analogs via click chemistry offer a new strategy for the development of stable antimicrobial agents. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Beijun Liu
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China.,School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Wei Zhang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Sanhu Gou
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Haifeng Huang
- Shaanxi Provincial People's Hospital, Shanxi, 710068, China
| | - Jia Yao
- The First Hospital of Lanzhou University, 199 West Donggang Road, Lanzhou, 730000, China
| | - Zhibin Yang
- Key Laboratory of Entomological Biopharmaceutical R&D of Yunnan Province, Dali University, Dali, 671000, China
| | - Hui Liu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Chao Zhong
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Beiyin Liu
- Affiliated Hospital of Gansu University of Chinese Medicine, Lanzhou, 730000, China
| | - Jingman Ni
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China.,School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Rui Wang
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
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Rautenbach M, Vlok NM, Eyéghé-Bickong HA, van der Merwe MJ, Stander MA. An Electrospray Ionization Mass Spectrometry Study on the "In Vacuo" Hetero-Oligomers Formed by the Antimicrobial Peptides, Surfactin and Gramicidin S. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1623-1637. [PMID: 28560564 DOI: 10.1007/s13361-017-1685-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
It was previously observed that the lipopeptide surfactants in surfactin (Srf) have an antagonistic action towards the highly potent antimicrobial cyclodecapeptide, gramicidin S (GS). This study reports on some of the molecular aspects of the antagonism as investigated through complementary electrospray ionization mass spectrometry techniques. We were able to detect stable 1:1 and 2:1 hetero-oligomers in a mixture of surfactin and gramicidin S. The noncovalent interaction between GS and Srf, with the proposed equilibrium: GS~Srf↔GS+Srf correlated to apparent K d values of 6-9 μM in gas-phase and 1 μM in aqueous solution. The apparent K d values decreased with a longer incubation time and indicated a slow oligomerization equilibrium. Furthermore, the low μM K dapp values of GS~Srf↔GS+Srf fell within the biological concentration range and related to the 2- to 3-fold increase in [GS] needed for bacterial growth inhibition in the presence of Srf. Competition studies indicated that neither Na+ nor Ca2+ had a major effect on the stability of preformed heterodimers and that GS in fact out-competed Ca2+ and Na+ from Srf. Traveling wave ion mobility mass spectrometry revealed near symmetrical peaks of the heterodimers correlating to a compact dimer conformation that depend on specific interactions. Collision-induced dissociation studies indicated that the peptide interaction is most probably between one Orn residue in GS and the Asp residue, but not the Glu residue in Srf. We propose that flanking hydrophobic residues in both peptides stabilize the antagonistic and inactive peptide hetero-oligomers and shield the specific polar interactions in an aqueous environment. Graphical Abstract ᅟ.
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Affiliation(s)
- Marina Rautenbach
- BIOPEP® Peptide Group, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa.
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa.
| | - N Maré Vlok
- BIOPEP® Peptide Group, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
| | - Hans A Eyéghé-Bickong
- BIOPEP® Peptide Group, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
| | - Marthinus J van der Merwe
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
- LCMS Central Analytical Facility, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
| | - Marietjie A Stander
- Department of Biochemistry, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
- LCMS Central Analytical Facility, University of Stellenbosch, Stellenbosch, 7602, Republic of South Africa
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Cyclic Peptides as Novel Therapeutic Microbicides: Engineering of Human Defensin Mimetics. Molecules 2017; 22:molecules22071217. [PMID: 28726740 PMCID: PMC6152268 DOI: 10.3390/molecules22071217] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 11/16/2022] Open
Abstract
Cyclic peptides are receiving significant attention thanks to their antimicrobial activity and high serum stability, which is useful to develop and design novel antimicrobial agents. Antimicrobial peptides appear to be key components of innate defences against bacteria, viruses, and fungi. Among the others, defensins possess a strong microbicidial activity. Defensins are cationic and amphipathic peptides with six cysteine residues connected by three disulfide bonds found in plants, insects, and mammals; they are divided in three families: α-, β-, and θ-defensins. α-Defensins are contained in the primary granules of human neutrophils; β-defensins are expressed in human epithelia; and θ-defensins are pseudo-cyclic defensins not found in humans, but in rhesus macaques. The structural diversities among the three families are reflected in a different antimicrobial action as well as in serum stability. The engineering of these peptides is an exciting opportunity to obtain more functional antimicrobial molecules highlighting their potential as therapeutic agents. The present review reports the most recent advances in the field of cyclic peptides with a specific regard to defensin analogs.
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Pal S, Ghosh U, Singh G, Alam F, Singh S, Chopra S, Sinha S, Ampapathi RS, Chakraborty TK. Synthesis, Conformational Studies and Biological Profiles of Tetrahydrofuran Amino-Acid-Containing Cationic Antitubercular Peptides. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sudip Pal
- Medicinal & Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Uttam Ghosh
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Gajendra Singh
- NMR Research Centre, Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Faiyaz Alam
- NMR Research Centre, Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Shyam Singh
- Biochemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Sidharth Chopra
- Microbiology Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Sudhir Sinha
- Biochemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Ravi Sankar Ampapathi
- NMR Research Centre, Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Tushar Kanti Chakraborty
- Medicinal & Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
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Pal S, Ghosh U, Ampapathi RS, Chakraborty TK. Recent Studies on Gramicidin S Analog Structure and Antimicrobial Activity. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/7081_2015_188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Liu Y, Mei L, Yu Q, Zhang Q, Gao H, Zhang Z, He Q. Integrin αvβ3 targeting activity study of different retro-inverso sequences of RGD and their potentiality in the designing of tumor targeting peptides. Amino Acids 2015; 47:2533-9. [DOI: 10.1007/s00726-015-2043-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 07/01/2015] [Indexed: 01/01/2023]
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23
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Tang W, Yuan H, Zhang H, Wang L, Qian H, Qi X. An antimicrobial peptide screened from casein hydrolyzate by Saccharomyces cerevisiae cell membrane affinity method. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.09.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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24
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Pal S, Singh G, Singh S, Tripathi JK, Ghosh JK, Sinha S, Ampapathi RS, Chakraborty TK. Tetrahydrofuran amino acid-containing gramicidin S analogues with improved biological profiles. Org Biomol Chem 2015; 13:6789-802. [DOI: 10.1039/c5ob00622h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Replacement of thed-Phe-Pro units of GS with novel C6-Bn-substituted tetrahydrofuran amino acid minimized its cytotoxicity while preserving its antimicrobial activity, with a few analogs showing selective anti-TB activity as well.
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Affiliation(s)
- Sudip Pal
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Gajendra Singh
- Centre for Nuclear Magnetic Resonance
- SAIF
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Shyam Singh
- Biochemistry Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Jitendra Kumar Tripathi
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Jimut Kanti Ghosh
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Sudhir Sinha
- Biochemistry Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Ravi Sankar Ampapathi
- Centre for Nuclear Magnetic Resonance
- SAIF
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Tushar Kanti Chakraborty
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
- Department of Organic Chemistry
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25
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Escobales N, Nuñez RE, Jang S, Parodi-Rullan R, Ayala-Peña S, Sacher JR, Skoda EM, Wipf P, Frontera W, Javadov S. Mitochondria-targeted ROS scavenger improves post-ischemic recovery of cardiac function and attenuates mitochondrial abnormalities in aged rats. J Mol Cell Cardiol 2014; 77:136-46. [PMID: 25451170 PMCID: PMC4312194 DOI: 10.1016/j.yjmcc.2014.10.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 10/14/2014] [Accepted: 10/17/2014] [Indexed: 01/21/2023]
Abstract
Mitochondria-generated reactive oxygen species (ROS) play a crucial role in the pathogenesis of aging and age-associated diseases. In this study, we evaluated the effects of XJB-5-131 (XJB), a mitochondria-targeted ROS and electron scavenger, on cardiac resistance to ischemia-reperfusion (IR)-induced oxidative stress in aged rats. Male adult (5-month old, n=17) and aged (29-month old, n=19) Fischer Brown Norway (F344/BN) rats were randomly assigned to the following groups: adult (A), adult+XJB (AX), aged (O), and aged+XJB (OX). XJB was administered 3 times per week (3mg/kg body weight, IP) for four weeks. At the end of the treatment period, cardiac function was continuously monitored in excised hearts using the Langendorff technique for 30 min, followed by 20 min of global ischemia, and 60-min reperfusion. XJB improved post-ischemic recovery of aged hearts, as evidenced by greater left ventricular developed-pressures and rate-pressure products than the untreated, aged-matched group. The state 3 respiration rates at complexes I, II and IV of mitochondria isolated from XJB-treated aged hearts were 57% (P<0.05), 25% (P<0.05) and 28% (P<0.05), respectively, higher than controls. Ca(2+)-induced swelling, an indicator of permeability transition pore opening, was reduced in the mitochondria of XJB-treated aged rats. In addition, XJB significantly attenuated the H2O2-induced depolarization of the mitochondrial inner membrane as well as the total and mitochondrial ROS levels in cultured cardiomyocytes. This study underlines the importance of mitochondrial ROS in aging-induced cardiac dysfunction and suggests that targeting mitochondrial ROS may be an effective therapeutic approach to protect the aged heart against IR injury.
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Affiliation(s)
- Nelson Escobales
- Department of Physiology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Rebeca E Nuñez
- Department of Physiology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Sehwan Jang
- Department of Physiology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Rebecca Parodi-Rullan
- Department of Physiology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Sylvette Ayala-Peña
- Department of Pharmacology and Toxicology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Joshua R Sacher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erin M Skoda
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Walter Frontera
- Department of Physiology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico; Department of Physical Medicine and Rehabilitation, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sabzali Javadov
- Department of Physiology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico.
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