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Waghu FH, Gawde U, Gomatam A, Coutinho E, Idicula‐Thomas S. A QSAR modeling approach for predicting myeloid antimicrobial peptides with high sequence similarity. Chem Biol Drug Des 2020; 96:1408-1417. [DOI: 10.1111/cbdd.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/20/2020] [Accepted: 06/14/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Faiza Hanif Waghu
- Biomedical Informatics Centre Indian Council of Medical Research‐National Institute for Research in Reproductive Health MumbaiIndia
| | - Ulka Gawde
- Biomedical Informatics Centre Indian Council of Medical Research‐National Institute for Research in Reproductive Health MumbaiIndia
| | - Anish Gomatam
- Molecular Simulations Group, Department of Pharmaceutical Chemistry Bombay College of Pharmacy MumbaiIndia
| | - Evans Coutinho
- Molecular Simulations Group, Department of Pharmaceutical Chemistry Bombay College of Pharmacy MumbaiIndia
| | - Susan Idicula‐Thomas
- Biomedical Informatics Centre Indian Council of Medical Research‐National Institute for Research in Reproductive Health MumbaiIndia
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2
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Avram S, Puia A, Udrea AM, Mihailescu D, Mernea M, Dinischiotu A, Oancea F, Stiens J. Natural Compounds Therapeutic Features in Brain Disorders by Experimental, Bioinformatics and Cheminformatics Methods. Curr Med Chem 2020; 27:78-98. [PMID: 30378477 DOI: 10.2174/0929867325666181031123127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/05/2018] [Accepted: 03/11/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Synthetic compounds with pharmaceutical applications in brain disorders are daily designed and synthesized, with well first effects but also seldom severe side effects. This imposes the search for alternative therapies based on the pharmaceutical potentials of natural compounds. The natural compounds isolated from various plants and arthropods venom are well known for their antimicrobial (antibacterial, antiviral) and antiinflammatory activities, but more studies are needed for a better understanding of their structural and pharmacological features with new therapeutic applications. OBJECTIVES Here we present some structural and pharmaceutical features of natural compounds isolated from plants and arthropods venom relevant for their efficiency and potency in brain disorders. We present the polytherapeutic effects of natural compounds belonging to terpenes (limonene), monoterpenoids (1,8-cineole) and stilbenes (resveratrol), as well as natural peptides (apamin, mastoparan and melittin). METHODS Various experimental and in silico methods are presented with special attention on bioinformatics (natural compounds database, artificial neural network) and cheminformatics (QSAR, drug design, computational mutagenesis, molecular docking). RESULTS In the present paper we reviewed: (i) recent studies regarding the pharmacological potential of natural compounds in the brain; (ii) the most useful databases containing molecular and functional features of natural compounds; and (iii) the most important molecular descriptors of natural compounds in comparison with a few synthetic compounds. CONCLUSION Our paper indicates that natural compounds are a real alternative for nervous system therapy and represents a helpful tool for the future papers focused on the study of the natural compounds.
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Affiliation(s)
- Speranta Avram
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Alin Puia
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Ana Maria Udrea
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Dan Mihailescu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Maria Mernea
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Anca Dinischiotu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Florin Oancea
- Bioproducts Lab, Bioresource Department, National Research and Development Institute for Chemistry and Petrochemistry, Bucharest, Romania
| | - Johan Stiens
- Department of Electronics and Informatics - ETRO, Vrije Universiteit Brussel, Brussels, Belgium
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3
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Limban C, Diţu LM, Măruțescu L, Missir AV, Chifiriuc MC, Căproiu MT, Morusciag L, Chiriţă C, Udrea AM, Nuţă DC, Avram S. Design, Synthesis and Biopharmacological Profile Evaluation of New 2-((4- Chlorophenoxy)Methyl)-N-(Arylcarbamothioyl)Benzamides with Broad Spectrum Antifungal Activity. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190621162950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The emerging antifungal resistance represents a major challenge for the treatment
of severe fungal infections, highlighting the need to develop novel and efficient antifungal
compounds. This study aimed to synthesize new title compounds and screen them
for their antifungal activity in order to generate highly accurate structure - activity relationships
of 2-((4-chlorophenoxy)methyl)-N-(arylcarbamothioyl)benzamides and their de novo
derivatives and to unveil some of their mechanisms of action by flow cytometry and fluorescence
microscopy. The presence of functional groups was confirmed for nine new 2-((4-
chlorophenoxy) methyl)-N-(arylcarbamothioyl)benzamides, using experimental and in silico
methods. The antifungal activity was assessed against a broad spectrum of 26 yeast and
filamentous fungal strains, using qualitative and quantitative assays. The results showed
that Candida kefyr has been the most susceptible to all tested compounds, while 1b and 1f induced a strong inhibitory
effect on the filamentous fungi Alternaria rubi, Aspergillus ochraceus and A. niger strains growth. The
derivative 1c in subinhibitory concentrations alsoincreased the susceptibility of Candida albicans clinical
strains to azoles. Predicted drug likeness and pharmacokinetics profiles of most active compounds were compared
with the standard antifungal ketoconazole. Furthermore, the potentially more potent 1c and 1f derivatives
were designed and studied regarding the chemical structure-biological activity relationship and pharmacokinetics
profiles versus ketoconazole. The study confirms that the new benzamide derivatives exhibited an improved
pharmacokinetics profile and a good antifungal activity, acting at least by increasing membrane permeability of
fungal cells. Our results are recommending them as promising candidates for the development of novel therapeutic
alternatives.
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Affiliation(s)
- Carmen Limban
- Department of Pharmaceutical Chemistry, “Carol Davila” University of Medicine and Pharmacy, Traian Vuia No. 6, Bucharest, 020956, Romania
| | - Lia M. Diţu
- Department of Botanic- Microbiology, Faculty of Biology, University of Bucharest, Research Institute of University of Bucharest- ICUB, Spl. Independentei no. 91-95, Bucharest, Romania
| | - Luminița Măruțescu
- Department of Botanic- Microbiology, Faculty of Biology, University of Bucharest, Research Institute of University of Bucharest- ICUB, Spl. Independentei no. 91-95, Bucharest, Romania
| | - Alexandru V. Missir
- Department of Pharmaceutical Chemistry, “Carol Davila” University of Medicine and Pharmacy, Traian Vuia No. 6, Bucharest, 020956, Romania
| | - Mariana C. Chifiriuc
- Department of Botanic- Microbiology, Faculty of Biology, University of Bucharest, Research Institute of University of Bucharest- ICUB, Spl. Independentei no. 91-95, Bucharest, Romania
| | - Miron T. Căproiu
- The Organic Chemistry Center, Romanian Academy “Costin D. Nenitescu, Splaiul Independentei, 202B, Bucharest, Romania
| | - Laurenţiu Morusciag
- Department of Pharmaceutical Chemistry, “Carol Davila” University of Medicine and Pharmacy, Traian Vuia No. 6, Bucharest, 020956, Romania
| | - Cornel Chiriţă
- Department of Pharmacology and Clinical Pharmacy, “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania
| | - Ana-Maria Udrea
- National Institute for Laser, Plasma and Radiation Physics, Magurele, Ilfov, Romania
| | - Diana C. Nuţă
- Department of Pharmaceutical Chemistry, “Carol Davila” University of Medicine and Pharmacy, Traian Vuia No. 6, Bucharest, 020956, Romania
| | - Speranta Avram
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Spl. Independentei no. 91-95, Bucharest, Romania
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Ritter SC, Yang ML, Kaznessis YN, Hackel BJ. Multispecies activity screening of microcin J25 mutants yields antimicrobials with increased specificity toward pathogenic Salmonella species relative to human commensal Escherichia coli. Biotechnol Bioeng 2018; 115:2394-2404. [PMID: 29940080 DOI: 10.1002/bit.26772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/05/2018] [Accepted: 06/18/2018] [Indexed: 12/13/2022]
Abstract
Modern large-scale agricultural practices that incorporate high density farming with subtherapeutic antibiotic dosing are considered a major contributor to the rise of antibiotic-resistant bacterial infections of humans with species of Salmonella being a leading agriculture-based bacterial infection. Microcin J25, a potent and highly stable antimicrobial peptide active against Enterobacteriaceae, is a candidate antimicrobial against multiple Salmonella species. Emerging evidence supports the hypothesis that the composition of the microbiota of the gastrointestinal tract prevents a variety of diseases by preventing infectious agents from proliferating. Reducing clearance of off-target bacteria may decrease susceptibility to secondary infection. Of the Enterobacteriaceae susceptible to microcin J25, Escherichia coli are the most abundant within the human gut. To explore the modulation of specificity, a collection of 207 mutants encompassing 12 positions in both the ring and loop of microcin J25 was built and tested for activity against Salmonella and E. coli strains. As has been found previously, mutational tolerance of ring residues was lower than loop residues, with 22% and 51% of mutations, respectively, retaining activity toward at least one target within the target organism test panel. The multitarget screening elucidated increased mutational tolerance at position G2, G3, and G14 than previously identified in panels composed of single targets. Multiple mutations conferred differential response between the different targets. Examination of specificity differences between mutants found that 30% showed significant improvements to specificity toward any of the targets. Generation and testing of a combinatorial library designed from the point-mutant study revealed that microcin J25I13T reduces off-target activity toward commensal human-derived E. coli isolates by 81% relative to Salmonella enterica serovar Enteritidis. These in vitro specificity improvements are likely to improve in vivo treatment efficacy by reducing clearance of commensal bacteria in the gastrointestinal tract of hosts.
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Affiliation(s)
- Seth C Ritter
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Mike L Yang
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota
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Howl J, Howl L, Jones S. The cationic tetradecapeptide mastoparan as a privileged structure for drug discovery: Enhanced antimicrobial properties of mitoparan analogues modified at position-14. Peptides 2018; 101:95-105. [PMID: 29337270 DOI: 10.1016/j.peptides.2018.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 01/01/2023]
Abstract
Mastoparan (MP) peptides, distributed in insect venoms, induce a local inflammatory response post envenomation. Most endogenous MPs share common structural elements within a tetradecapeptide sequence that adopts an amphipathic helix whilst traversing biological membranes and when bound to an intracellular protein target. Rational modifications to increase cationic charge density and amphipathic helicity engineered mitoparan (MitP), a mitochondriotoxic bioportide and potent secretagogue. Following intracellular translocation, MitP is accreted by mitochondria thus indicating additional utility as an antimicrobial agent. Hence, the objectives of this study were to compare the antimicrobial activities of a structurally diverse set of cationic cell penetrating peptides, including both MP and MitP sequences, and to chemically engineer analogues of MitP for potential therapeutic applications. Herein, we confirm that, like MP, MitP is a privileged structure for the development of antimicrobial peptides active against both prokaryotic and eukaryotic pathogens. Collectively, MitP and target-selective chimeric analogues are broad spectrum antibiotics, with the Gram-negative A. baumannii demonstrating particular susceptibility. Modifications of MitP by amino acid substitution at position-14 produced peptides, Δ14MitP analogues, with unique pharmacodynamic properties. One example, [Ser14]MitP, lacks both cytotoxicity against human cell lines and mast cell secretory activity yet retains selective activity against the encapsulated yeast C. neoformans.
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Affiliation(s)
- John Howl
- Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY, United Kingdom.
| | - Lewis Howl
- Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY, United Kingdom
| | - Sarah Jones
- Research Institute in Healthcare Science, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY, United Kingdom
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Mikut R, Ruden S, Reischl M, Breitling F, Volkmer R, Hilpert K. Improving short antimicrobial peptides despite elusive rules for activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1024-33. [PMID: 26687790 DOI: 10.1016/j.bbamem.2015.12.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/25/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
Antimicrobial peptides (AMPs) can effectively kill a broad range of life threatening multidrug-resistant bacteria, a serious threat to public health worldwide. However, despite great hopes novel drugs based on AMPs are still rare. To accelerate drug development we studied different approaches to improve the antibacterial activity of short antimicrobial peptides. Short antimicrobial peptides seem to be ideal drug candidates since they can be synthesized quickly and easily, modified and optimized. In addition, manufacturing a short peptide drug will be more cost efficient than long and structured ones. In contrast to longer and structured peptides short AMPs seem hard to design and predict. Here, we designed, synthesized and screened five different peptide libraries, each consisting of 600 9-mer peptides, against Pseudomonas aeruginosa. Each library is presenting a different approach to investigate effectiveness of an optimization strategy. The data for the 3000 peptides were analyzed using models based on fuzzy logic bioinformatics and plausible descriptors. The rate of active or superior active peptides was improved from 31.0% in a semi-random library from a previous study to 97.8% in the best new designed library. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.
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Affiliation(s)
- Ralf Mikut
- Karlsruhe Institute of Technology (KIT), Institute for Applied Computer Science, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Serge Ruden
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces and Institute of Biological Interfaces 2, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Markus Reischl
- Karlsruhe Institute of Technology (KIT), Institute for Applied Computer Science, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Frank Breitling
- Karlsruhe Institute of Technology (KIT), Institute of Microstructure Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Rudolf Volkmer
- Institute of Medical Immunology, Universitätsklinikum Charité, Humboldt-Universität zu Berlin, Schumannstr. 20-21, 10117 Berlin, Germany
| | - Kai Hilpert
- Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces and Institute of Biological Interfaces 2, P.O. Box 3640, 76021 Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Institute of Microstructure Technology, P.O. Box 3640, 76021 Karlsruhe, Germany; Institute of Infection and Immunity, St. George's University of London, Cranmer Terrace, London, SW17 0RE, United Kingdom.
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7
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Toropova MA, Veselinović AM, Veselinović JB, Stojanović DB, Toropov AA. QSAR modeling of the antimicrobial activity of peptides as a mathematical function of a sequence of amino acids. Comput Biol Chem 2015; 59 Pt A:126-30. [DOI: 10.1016/j.compbiolchem.2015.09.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 08/04/2015] [Accepted: 09/15/2015] [Indexed: 01/29/2023]
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Structure-biological function relationship extended to mitotic arrest-deficient 2-like protein Mad2 native and mutants-new opportunity for genetic disorder control. Int J Mol Sci 2014; 15:21381-400. [PMID: 25411801 PMCID: PMC4264231 DOI: 10.3390/ijms151121381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 02/07/2023] Open
Abstract
Overexpression of mitotic arrest-deficient proteins Mad1 and Mad2, two components of spindle assembly checkpoint, is a risk factor for chromosomal instability (CIN) and a trigger of many genetic disorders. Mad2 transition from inactive open (O-Mad2) to active closed (C-Mad2) conformations or Mad2 binding to specific partners (cell-division cycle protein 20 (Cdc20) or Mad1) were targets of previous pharmacogenomics studies. Here, Mad2 binding to Cdc20 and the interconversion rate from open to closed Mad2 were predicted and the molecular features with a critical contribution to these processes were determined by extending the quantitative structure-activity relationship (QSAR) method to large-size proteins such as Mad2. QSAR models were built based on available published data on 23 Mad2 mutants inducing CIN-related functional changes. The most relevant descriptors identified for predicting Mad2 native and mutants action mechanism and their involvement in genetic disorders are the steric (van der Waals area and solvent accessible area and their subdivided) and energetic van der Waals energy descriptors. The reliability of our QSAR models is indicated by significant values of statistical coefficients: Cross-validated correlation q2 (0.53–0.65) and fitted correlation r2 (0.82–0.90). Moreover, based on established QSAR equations, we rationally design and analyze nine de novo Mad2 mutants as possible promoters of CIN.
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Bacalum M, Radu M. Cationic Antimicrobial Peptides Cytotoxicity on Mammalian Cells: An Analysis Using Therapeutic Index Integrative Concept. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9430-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Chondroitin sulfate proteoglycans: structure-function relationship with implication in neural development and brain disorders. BIOMED RESEARCH INTERNATIONAL 2014; 2014:642798. [PMID: 24955366 PMCID: PMC4052930 DOI: 10.1155/2014/642798] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/28/2014] [Accepted: 04/28/2014] [Indexed: 12/12/2022]
Abstract
Chondroitin sulfate proteoglycans (CSPGs) are extracellular matrix components that contain two structural parts with distinct functions: a protein core and glycosaminoglycan (GAG) side chains. CSPGs are known to be involved in important cell processes like cell adhesion and growth, receptor binding, or cell migration. It is recognized that the presence of CSPGs is critical in neuronal growth mechanisms including axon guidance following injury of nervous system components such as spinal cord and brain. CSPGs are upregulated in the central nervous system after injury and participate in the inhibition of axon regeneration mainly through their GAG side chains. Recently, it was shown that some CSPGs members like aggrecan, versican, and neurocan were strongly involved in brain disorders like bipolar disorder (BD), schizophrenia, and ADHD. In this paper, we present the chemical structure-biological functions relationship of CSPGs, both in health state and in genetic disorders, addressing methods represented by genome-wide and crystallographic data as well as molecular modeling and quantitative structure-activity relationship.
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Avram S, Milac AL, Carta F, Supuran CT. More effective dithiocarbamate derivatives inhibiting carbonic anhydrases, generated by QSAR and computational design. J Enzyme Inhib Med Chem 2012; 28:350-9. [DOI: 10.3109/14756366.2012.727410] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Speranta Avram
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Romania
| | | | - Fabrizio Carta
- Laboratorio di Chimica Bioinorganica, Polo Scientifico, Universita degli Studi di Firenze,
Sesto Fiorentino, Florence, Italy
| | - Claudiu T. Supuran
- Laboratorio di Chimica Bioinorganica, Polo Scientifico, Universita degli Studi di Firenze,
Sesto Fiorentino, Florence, Italy
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Firenze,
Sesto Fiorentino, Florence, Italy
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Avram S, Mihailescu D, Borcan F, Milac AL. Prediction of improved antimicrobial mastoparan derivatives by 3D-QSAR-CoMSIA/CoMFA and computational mutagenesis. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-011-0713-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Avram S, Buiu C, Borcan F, Milac AL. More effective antimicrobial mastoparan derivatives, generated by 3D-QSAR-Almond and computational mutagenesis. ACTA ACUST UNITED AC 2012; 8:587-94. [DOI: 10.1039/c1mb05297g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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