Download or read book Design of Highly Active Antimicrobial Peptides Using Mathematical and Computer Modeling written by Naveen Pathak and published by . This book was released on 1994 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Masters Theses in the Pure and Applied Sciences written by Wade H. Shafer and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Masters Theses in the Pure and Applied Sciences was first conceived, published, and disseminated by the Center for Information and Numerical Data Analysis and Synthesis (CINDAS)* at Purdue University in 1957, starting its coverage of theses with the academic year 1955. Beginning with Volume 13, the printing and dis semination phases of the activity were transferred to University Microfilms/Xerox of Ann Arbor, Michigan, with the thought that such an arrangement would be more beneficial to the academic and general scientific and technical community. After five years of this joint undertaking we had concluded that it was in the interest of all concerned if the printing and distribution of the volumes were handled by an international publishing house to assure improved service and broader dissemination. Hence, starting with Volume 18, Masters Theses in the Pure and Applied Sciences has been disseminated on a worldwide basis by Plenum Publishing Corporation of New York, and in the same year the coverage was broadened to include Canadian universities. All back issues can also be ordered from Plenum. We have reported in Volume 39 (thesis year 1994) a total of 13,953 thesis titles from 21 Canadian and 159 United States universities. We are sure that this broader base for these titles reported will greatly enhance the value of this impor tant annual reference work. While Volume 39 reports theses submitted in 1994, on occasion, certain uni versities do report theses submitted in previous years but not reported at the time.
Download or read book Antimicrobial Peptides written by Andrea Giuliani and published by Humana Press. This book was released on 2011-08-25 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: The action of antimicrobial peptides (AMPs), ranging from direct killing of invading pathogens to immune response modulation and other complex biological responses, has stimulated research and clinical interest for more than two decades, but the area is still burgeoning due to emerging discoveries in the functions, roles, and regulation of AMPs, thus making the study of antimicrobial peptides a multi-disciplinary and rapidly evolving field. In Antimicrobial Peptides: Methods and Protocols, leading investigators present a broad, up-to-date collection of current research and experimental methods for the isolation, characterization, production, and optimization of antimicrobial peptides. Additional chapters detail methodologies in several microscopy techniques, high-throughput screening, QSAR modeling, and computer-aided design used to study these compounds, while key review articles survey potential medical applications of antimicrobial peptides as innovative anti-infective and immunomodulatory agents, as well as emerging discoveries in their function, regulation, and roles in innate immunity. As a volume in the highly successful Methods in Molecular BiologyTM series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and wide-ranging in its applications, Antimicrobial Peptides: Methods and Protocols provides both an authoritative guide for lab work on AMPs or related substances and a useful collection of thought stimuli to inspire further scientific endeavours in a wide array of vital fields.
Download or read book Delivery Design and Mechanism of Antimicrobial Peptides written by Tanguy Chau and published by . This book was released on 2010 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt: Each year, 2 million people contract hospital-acquired bacterial infections, which causes the death of 100,000 patients and costs the US healthcare system over $21 billion. These infections have become dangerously resistant to our existing line of antibiotics and are rapidly spreading outside of hospitals and into communities. As molecular targets to develop new antibiotics are becoming exhausted, clinicians and scientist are concerned that antibiotic resistant infections will wipe out most of the major health benefits acquired over the last century. The work described in this thesis develops new antimicrobials strategies against bacterial infections, focusing on antimicrobial peptides (AmPs). We first delivered genes inducing the toxic expression of AmPs and other lytic agents directly into bacteria using re-engineered bacteriophages. Expression of these lytic agents in lysogenic bacteriophages resulted in bactericidal activity, and demonstrated, for the first time, a long-term cidal effect for over 20 hours. We then enhanced the efficacy of our approach by expressing the same agents in lytic bacteriophage, which resulted in complete suppression of the bacterial culture and prevented bacterial regrowth and resistance to bacteriophages. Since a large fraction of medical infections originates at the surface of implantable devices, we developed film coatings that release active AmPs to cover these surfaces and prevent bacterial colonization. We incorporated AmPs in layer-by-layer films and demonstrated that the kinetics of AmP release can be adjusted. These released AmPs still actively prevented bacterial growth and remained non-toxic towards mammalian cells. While natural AmPs have broad activity against pathogens, they are not optimized for a specific antimicrobial function or bacterial target. Thus, researchers have tried for decades to design highly active and specific de novo AmPs. One approach is to design new peptides using conserved motifs identified from the amino acid sequence of natural AmPs. We improved this approach by measuring the antimicrobial activity of a large database of natural AmPs and incorporating this activity information in the design algorithm. This strategy improved the success rate of designing de novo peptides from 45% to 73% and increased the antimicrobial strength of the designed peptides. Finally, we developed new potentiating strategies by studying the mode-of-action of the family of ponericin AmPs. First, we measured their cidal behavior and differentiated bactericidal ponericins from bacteriostatic ones. Using a modified AFM and a microfluidic device, we observed that the action of AmPs led to cellular death through the corrugation of bacterial, while subpopulation of cells resisted the action of the AmPs longer than others. Focusing on the ponericin G1 AmP, we correlated these visual observations with various membrane stress sensing mechanisms. We concluded that bacteria's ability to develop resistance to ponericin G1 requires the sensing and repair of misfolded membrane proteins via the CpxAR system, as well as DNA repair via induction of the SOS response by RecA. Using microarrarys, we showed that ponericin G1 targets tRNA synthetases in the ribosome. Finally, we demonstrated 99.999% killing of antibiotic resistant bacteria by potentiating ponericin G1 with the ribosomal antibiotic kanamycin, whereas no killing is observed when these two agents are applied independently. untreta The PhDCEP capstone requirement finalizes the work of this thesis by analyzing market entry and expansion strategies for an antimicrobial company commercializing genetically engineered bacteriophages. In conclusion, this thesis establishes new advances in the delivery, the design and the potentiation of AmPs in order to eradicate resilient bacterial infections.
Download or read book Master s Theses Directories written by and published by . This book was released on 1994 with total page 590 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Education, arts and social sciences, natural and technical sciences in the United States and Canada".
Download or read book Antimicrobial Peptides written by David A. Phoenix and published by John Wiley & Sons. This book was released on 2012-12-27 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this text, the small team of expert authors presents the field in a comprehensive and accessible manner that is well suited for students and junior researchers. The result is a highly readable and systematically structured introduction to antimicrobial peptides, their structure, biological function and mode of action. The authors point the way towards a rational design of this potentially highly effective new class of clinical antibiotics on the brink of industrial application. They do this by discussing their design principles, target membranes and structure-activity relationships. The final part of the book describes recent successes in the application of peptides as anticancer agents.
Download or read book Antimicrobial Peptides written by Katsumi Matsuzaki and published by Springer. This book was released on 2019-04-12 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of antimicrobial peptides (AMPs), their mechanisms of antimicrobial action, other activities, and various problems that must still be overcome regarding their clinical application. Divided into four major parts, the book begins with a general overview of AMPs (Part I), and subsequently discusses the various mechanisms of antimicrobial action and methods for researching them (Part 2). It then addresses a range of activities other than antimicrobial action, such as cell penetration, antisepsis, anticancer, and immunomodulatory activities (Part 3), and explores the prospects of clinical application from various standpoints such as the selective toxicity, design, and discovery of AMPs (Part 4). A huge number of AMPs have been discovered in plants, insects, and vertebrates including humans, and constitute host defense systems against invading pathogenic microorganisms. Consequently, many attempts have been made to utilize AMPs as antibiotics. AMPs could help to solve the urgent problem of drug-resistant bacteria, and are also promising with regard to sepsis and cancer therapy. Gathering a wealth of information, this book will be a bible for all those seeking to develop antibiotics, anti-sepsis, or anticancer agents based on AMPs.
Download or read book Computer Aided Design of Antimicrobial Lipopeptides as Prospective Drug Candidates written by Jujjvarapu Satya Eswari and published by CRC Press. This book was released on 2019-09-24 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt: Increase in antibiotic resistance has forced researchers to develop new drugs against microorganisms. Lipopeptides are produced as secondary metabolites by some microorganisms. Computer-aided Design of Antimicrobial Lipopeptides as Prospective Drug Candidates provides the identification of novel ligands for different antimicrobial lipopeptides. Along with identification, it also provides some of the in silico drug design processes, namely homology modelling, molecular docking, QSAR studies, drug ADMET studies and pharmacophore studies to check the ligand-lipopeptide interaction. Some lipopeptides have shown anti-cancerous properties too, and this book discusses the required templates to design new drugs using computational techniques. Key Features: Focuses on the use lipopeptides as new antimicrobial compounds Presents the basics of in silico modelling for design and development of new drug molecules, and is therefore of interest to beginners in the field Provides a step-by-step process for identification of drug molecules and testing its efficacy in silico Couples with courses on patents and intellectual property rights
Download or read book Antimicrobial Peptides written by and published by Academic Press. This book was released on 2022-02-12 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Antimicrobial Peptides, Volume 663 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on Unifying the classification of antimicrobial peptides in the Antimicrobial Peptide Database, Optimizing peptide library creation for PepSAVI-MS (RP libraries, etc.), Discovery of novel Antimicrobial peptides using BioProspecting, Screening for cysteine-stabilized scaffolds for developing protelytic-resistant AMPs, Exploring synergy and its role in antimicrobial peptide biology, Colorimetric assays for the rapid and high-throughput screening of antimicrobial peptide activity against diverse bacterial pathogens, and much more. Other chapters cover Liquid chromatography-mass spectrometry-based analysis of naturally occurring neuropeptide diastereomers, Multiplexed Quantitative Neuropeptidomics via DiLeu Isobaric Tagging, In vitro evaluation of antibiotic resistance via proteomics, Molecular networking-based strategies in mass spectrometry, Development of Macrocyclic antimicrobial peptides and peptoids, and a host of other timely topics. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in Methods in Enzymology serials Updated release includes the latest information on Antimicrobial Peptides
Download or read book Computational Approaches in Discovery Design of Antimicrobial Peptides written by Agostinho Agüero-Chapin and published by Mdpi AG. This book was released on 2023-06-19 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Antimicrobial resistance remains a major concern in medicine, especially during the COVID-19 pandemic, where microbial infections were frequent complications. To combat drug-resistant pathogens, there has been a renewed interest in the use of antimicrobial peptides (AMPs). This reprint focuses on the in-silico approaches used for the rational discovery and design of AMPs. Such computational methodologies range from classical homology-based and machine-learning prediction algorithms to complex similarity networks and evolutionary algorithms that use models of sequence evolution. Furthermore, the reprint explores the improvement of high-throughput screening techniques in the discovery of AMPs from biological samples, which has also led to the evolution of computational approaches that aid in this biodiscovery process. The reprint contains original research and review papers, which serve as valuable references for researchers dedicated to peptide drug development.
Download or read book Computational Peptide Science written by Thomas Simonson and published by Humana. This book was released on 2023-04-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details current and new computational methodologies to study peptides. Chapters guide readers through antimicrobial peptides, foldability, amyloid sheet formation, membrane-active peptides, organized peptide assemblies, protein-peptide interfaces, prediction of peptide-MHC complexes, advanced free energy simulations for peptide binding, and methods for high throughput peptide or miniprotein design. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, software, and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Computational Peptides Science: Methods and Protocols aims to provide concepts, methods, and guidelines to help both novices and experienced workers benefit from today's new opportunities and challenges.
Download or read book Antimicrobial Peptides written by Guangshun Wang and published by CABI. This book was released on 2017-09-01 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: Antimicrobial peptides (AMPs) have attracted extensive research attention worldwide. Harnessing and creating AMPs synthetically has the potential to help overcome increasing antibiotic resistance in many pathogens. This new edition lays the foundations for studying AMPs, including a discovery timeline, terminology, nomenclature and classifications. It covers current advances in AMP research and examines state-of-the-art technologies such as bioinformatics, combinatorial libraries, high-throughput screening, database-guided identification, genomics and proteomics-based prediction, and structure-based design of AMPs. Thoroughly updated and revised, this second edition contains new content covering: defensins; cathelicidins; anti-MRSA, antifungal, antiviral, anticancer and antibiofilm strategies; combined treatments; adjuvants in vaccines; advances in AMP technologies that cover surface coating to prevent biofilm formation; nanofiber encapsulation technologies for delivery and sustained release; and understanding innate immunity and the basis for immune boosting to overcome obstacles in developing AMPs into therapeutic agents. Written and reviewed by a group of established investigators in the field, Antimicrobial Peptides is a valuable resource for postgraduate students, researchers, educators, and medical and industrial personnel.
Download or read book Progress Toward the Computational Design of Tighter binding Antimicrobial Peptides Based on Buforin II written by Qiao Li and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The extensive and universal use of antibiotics for humans and livestock has resulted in the worldwide emergence of antibiotic-resistant bacteria, causing thousands of deaths per year in the US. Antimicrobial peptides (AMPs) are studied as alternative therapeutics for their natural antimicrobial properties and a low tendency of developing resistant bacteria. This study aims to design improved AMPs using the naturally occurring cationic AMP buforin II (BF2) as a modeling template. BF2 enters bacterial cells and binds to the DNA, killing the microorganisms by disrupting critical intracellular processes. Accordingly, this study focuses on strengthening the dominant factor, electrostatic attraction, that drives the BF2-DNA binding through increasing the overall net charge of BF2 with an arginine substitution for a neutral amino acid residue. Partial charge optimization is used here to help determine which natural BF2 residues to mutate for maximal effect. Then, molecular dynamics simulations are employed to further evaluate the binding free energy of promising arginine-substituted BF2 variants to DNA. Based on the computational results, T1R BF2 was selected as a promising candidate. Several BF2 variants (L19R, Q9R, Q9R/H16F, A6R, and L8R BF2) were examined to find negative control. L8R BF2 was chosen as a potential negative control and other BF2 variants were not consider further due to the insignificant differences in the binding free energy comparing to T1R BF2. To validate the modeling effects, future work includes characterizing the binding affinity of these BF2 variants to DNA using fluorescent interchelator displacement assays.
Download or read book Synthetic Mimics of Antimicrobial Peptides from Aryl Scaffolds written by Hitesh Thaker and published by . This book was released on 2013 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: The rise in bacterial resistance and the declining approval rate of novel anti-infective drugs are a major threat to global public health. Antimicrobial peptides (AMPs), found in almost every multicellular organism, have attracted considerable attention as models for the design of new therapeutic agents due to their broad spectrum activity and reduced bacterial resistance development. This dissertation focuses on the development of a new series of synthetic mimics of antimicrobial peptides (SMAMPs) from simple aryl scaffolds using Suzuki Miyaura coupling. This novel design allows easy tuning of the conformation, overall hydrophobicity of the molecule, amphiphilicity, and the number of charges in order to develop a structure-activity relationship. The antimicrobial activities of the SMAMPs against both gram-positive and gram-negative bacteria suggest that improving the selectivity requires fine-tuning of one or more of these parameters, with overall hydrophobicity and charge having a more significant impact than conformational rigidity. Furthermore, comparing the activities of SMAMPS with facially amphiphilic and disrupted amphiphilic topologies confirmed that amphiphilicity is an important design parameter for attaining antimicrobial activity, especially against gram-negative bacteria. This aryl scaffold design has led to the development of several highly active SMAMPs with selectivities>200 against both gram-positive S. aureus and gram-negative E. coli, which is nearly 20 times higher than that of the conventional AMP, MSI-78. One of these SMAMPs also shows a unique immunomodulatory response involving the induction of both cytokines and chemokines, which can have significant therapeutic potential. Similar chemistry was employed in the development of novel lipopeptide mimics (LPMs), where the attachment of pendant aliphatic chains to the tri-aryl backbone structure can be used to modulate the activity. The second project in this dissertation concerns the investigation of the influence of the cobalt density in the phase-separated domains in the ferromagnetic block copolymer materials A series of metal-containing block-random copolymers composed of an alkyl-functionalized homo block (C 16) and a random block of cobalt complex- (Co) and ferrocene complex-functionalized (Fe) units was synthesized via ring-opening metathesis polymerization (ROMP). Taking advantage of the block-random architecture, the influence of dipolar interactions on the magnetic properties of these nanostructured BCPs was studied by systematically varying the molar ratio of the Co units to the Fe units, while maintaining the cylindrical phase-separated morphology. A decrease in the cobalt density weakens the dipolar interactions between the cobalt nanoparticles, leading to the transition from a room temperature ferromagnetic material to a superparamagnetic material. These results confirm that the dipolar interactions of the cobalt nanoparticles within the phase-separated domains are responsible for the (unexpected) room temperature ferromagnetic properties of the nanostructured BCPs.
Download or read book Systems Medicine written by and published by Academic Press. This book was released on 2020-08-24 with total page 1571 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information
Download or read book Design Characterization and Molecular Dynamics Simulations of Antimicrobial Peptides written by 蔡政育 and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Drug Design written by D. C. Young and published by John Wiley & Sons. This book was released on 2009-01-28 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Helps you choose the right computational tools and techniques to meet your drug design goals Computational Drug Design covers all of the major computational drug design techniques in use today, focusing on the process that pharmaceutical chemists employ to design a new drug molecule. The discussions of which computational tools to use and when and how to use them are all based on typical pharmaceutical industry drug design processes. Following an introduction, the book is divided into three parts: Part One, The Drug Design Process, sets forth a variety of design processes suitable for a number of different drug development scenarios and drug targets. The author demonstrates how computational techniques are typically used during the design process, helping readers choose the best computational tools to meet their goals. Part Two, Computational Tools and Techniques, offers a series of chapters, each one dedicated to a single computational technique. Readers discover the strengths and weaknesses of each technique. Moreover, the book tabulates comparative accuracy studies, giving readers an unbiased comparison of all the available techniques. Part Three, Related Topics, addresses new, emerging, and complementary technologies, including bioinformatics, simulations at the cellular and organ level, synthesis route prediction, proteomics, and prodrug approaches. The book's accompanying CD-ROM, a special feature, offers graphics of the molecular structures and dynamic reactions discussed in the book as well as demos from computational drug design software companies. Computational Drug Design is ideal for both students and professionals in drug design, helping them choose and take full advantage of the best computational tools available. Note: CD-ROM/DVD and other supplementary materials are not included as part of eBook file.
