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Special Issue "Molecular Diversity Feature Papers"

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Diversity".

Deadline for manuscript submissions: closed (31 October 2009)

Special Issue Editors

Guest Editor
Dr. Derek J. McPhee

Senior Director, Technology Strategy, Amyris, Inc., 5885 Hollis St, Suite 100, Emeryville, CA 94608, USA
E-Mail
Fax: +1 510 225 2645
Interests: organic synthesis; medicinal chemistry; biotechnology
Editorial Advisor
Dr. Shu-Kun Lin

MDPI AG, St. Alban-Anlage 66, CH-4052 Basel, Switzerland
Website | E-Mail
Interests: Gibbs paradox; entropy; symmetry; similarity; diversity; information theory; thermodynamics; process irreversibility or spontaneity; stability; nature of the chemical processes; molecular recognition; open access journals

Keywords

  • synthesis of compound libraries
  • screen design and advanced technology
  • miniature, automation and instrumentation
  • coupling of synthesis and screening of compound libraries
  • analytical characterization studies
  • sample management
  • strategies for information management
  • virtual screening
  • library design and diversity assessment
  • chemoinformatics
  • databases
  • molecular similarity
  • diversity assessment
  • high-throughput functional screens

Published Papers (7 papers)

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Research

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Open AccessArticle Generation of 500-Member Library of 10-Alkyl-2-R1,3-R2-4,10-Dihydrobenzo[4,5]imidazo[1,2-α]pyrimidin-4-ones
Molecules 2009, 14(12), 5223-5234; doi:10.3390/molecules14125223
Received: 4 November 2009 / Revised: 3 December 2009 / Accepted: 14 December 2009 / Published: 15 December 2009
Cited by 5 | PDF Full-text (176 KB)
Abstract
Representative benzimidazopyrimidinones were previously reported to be intercalating antitumor agents. In this work, we used 2-substituted 4,10-dihydrobenzo [4,5]imidazo[1,2-α]pyriminin-4-ones for their diversification by regioselective alkylation. Under the conditions established, the alkylation gave 10-alkyl derivatives which permitted the parallel generation of a 500-member
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Representative benzimidazopyrimidinones were previously reported to be intercalating antitumor agents. In this work, we used 2-substituted 4,10-dihydrobenzo [4,5]imidazo[1,2-α]pyriminin-4-ones for their diversification by regioselective alkylation. Under the conditions established, the alkylation gave 10-alkyl derivatives which permitted the parallel generation of a 500-member library of the title compounds. Full article
(This article belongs to the Special Issue Molecular Diversity Feature Papers)
Open AccessArticle Pore Forming Properties of Cecropin-Melittin Hybrid Peptide in a Natural Membrane
Molecules 2009, 14(12), 5179-5188; doi:10.3390/molecules14125179
Received: 2 November 2009 / Revised: 4 December 2009 / Accepted: 10 December 2009 / Published: 11 December 2009
Cited by 8 | PDF Full-text (377 KB)
Abstract
The pore forming properties of synthetic cecropin-melittin hybrid peptide (Acetyl-KWKLFKKIGAVLKVL-CONH2; CM15) were investigated by using photoreceptor rod outer segments (OS) isolated from frog retinae obtained by using the whole-cell configuration of the patch-clamp technique. CM15 was applied (and removed) to
[...] Read more.
The pore forming properties of synthetic cecropin-melittin hybrid peptide (Acetyl-KWKLFKKIGAVLKVL-CONH2; CM15) were investigated by using photoreceptor rod outer segments (OS) isolated from frog retinae obtained by using the whole-cell configuration of the patch-clamp technique. CM15 was applied (and removed) to (from) the OS in ~50 ms with a computer-controlled microperfusion system. Once the main OS endogenous conductance was blocked with light, the OS membrane resistance was ≥1 GΩ, allowing high resolution, low-noise recordings. Different to alamethicines, CM15 produced voltage-independent membrane permeabilisation, repetitive peptide application caused a progressive permeabilisation increase, and no single-channel events were detected at low peptide concentrations. Collectively, these results indicate a toroidal mechanism of pore formation by CM15. Full article
(This article belongs to the Special Issue Molecular Diversity Feature Papers)
Open AccessArticle Chemosystematic Value of the Essential Oil Composition of Thuja species Cultivated in Poland—Antimicrobial Activity
Molecules 2009, 14(11), 4707-4715; doi:10.3390/molecules14114707
Received: 21 October 2009 / Revised: 5 November 2009 / Accepted: 9 November 2009 / Published: 19 November 2009
Cited by 23 | PDF Full-text (218 KB)
Abstract
In the framework of the correlation between chemotaxonomy and chemical analysis studies, the chemical composition of the essential oils of four varieties of Thuja species cultivated in Poland − T. occidentalis ‘globosa’, T. occidentalis ‘aurea’, T. plicata and T. plicata ‘gracialis’
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In the framework of the correlation between chemotaxonomy and chemical analysis studies, the chemical composition of the essential oils of four varieties of Thuja species cultivated in Poland − T. occidentalis ‘globosa’, T. occidentalis ‘aurea’, T. plicata and T. plicata ‘gracialis’ − were investigated by GC and GC-MS. Thirty-one compounds were identified from T. occidentalis ‘globosa’, representing 96.92% of the total oil; twenty-seven from T. occidentalis ‘aurea’ (94.34%); thirty-one from T. plicata (94.75%); and thirty compounds from T. plicata ‘gracialis’ (96.36%). The main constituents in all samples were the monoterpene ketones α- and β-thujone, fenchone and sabinene, as well as the diterpenes beyerene and rimuene.The chemosystematic value of the total ketone content of all samples (which varied from 54.30–69.18%) has been discussed and investigated. The constituents, beyerene and the mixture of α- and β-thujone, were isolated from the oils and tested against six Gram-positive and -negative bacteria and three pathogenic fungi. The oils of the two T. plicata species exhibited significant antimicrobial activity, while the mixture of α- and β-thujone showed very strong activity as well. Full article
(This article belongs to the Special Issue Molecular Diversity Feature Papers)
Open AccessArticle Headspace, Volatile and Semi-Volatile Organic Compounds Diversity and Radical Scavenging Activity of Ultrasonic Solvent Extracts from Amorpha fruticosa Honey Samples
Molecules 2009, 14(8), 2717-2728; doi:10.3390/molecules14082717
Received: 10 July 2009 / Revised: 23 July 2009 / Accepted: 27 July 2009 / Published: 27 July 2009
Cited by 23 | PDF Full-text (430 KB)
Abstract
Volatile organic compounds of Amorpha fruticosa honey samples were isolated by headspace solid-phase microextraction (HS-SPME) and ultrasonic solvent extraction (USE), followed by gas chromatography and mass spectrometry analyses (GC, GC-MS), in order to obtain complementary data for overall characterization of the honey aroma.
[...] Read more.
Volatile organic compounds of Amorpha fruticosa honey samples were isolated by headspace solid-phase microextraction (HS-SPME) and ultrasonic solvent extraction (USE), followed by gas chromatography and mass spectrometry analyses (GC, GC-MS), in order to obtain complementary data for overall characterization of the honey aroma. The headspace of the honey was dominated by 2-phenylethanol (38.3–58.4%), while other major compounds were trans- and cis-linalool oxides, benzaldehyde and benzyl alcohol. 2-Phenylethanol (10.5–16.8%) and methyl syringate (5.8–8.2%) were the major compounds of ultrasonic solvent extracts, with an array of small percentages of linalool, benzene and benzoic acid derivatives, aliphatic hydrocarbons and alcohols, furan derivatives and others. The scavenging ability of the series of concentrations of the honey ultrasonic solvent extracts and the corresponding honey samples was tested by a DPPH (1,1-diphenyl-2-picrylhydrazyl) assay. Approximately 25 times lower concentration ranges (up to 2 g/L) of the extracts exhibited significantly higher free radical scavenging potential with respect to the honey samples. Full article
(This article belongs to the Special Issue Molecular Diversity Feature Papers)
Open AccessArticle On Two Novel Parameters for Validation of Predictive QSAR Models
Molecules 2009, 14(5), 1660-1701; doi:10.3390/molecules14051660
Received: 16 April 2009 / Accepted: 28 April 2009 / Published: 29 April 2009
Cited by 262 | PDF Full-text (235 KB) | Correction | Supplementary Files
Abstract
Validation is a crucial aspect of quantitative structure–activity relationship (QSAR) modeling. The present paper shows that traditionally used validation parameters (leave-one-out Q2 for internal validation and predictive R2 for external validation) may be supplemented with two novel parameters rm2
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Validation is a crucial aspect of quantitative structure–activity relationship (QSAR) modeling. The present paper shows that traditionally used validation parameters (leave-one-out Q2 for internal validation and predictive R2 for external validation) may be supplemented with two novel parameters rm2 and Rp2 for a stricter test of validation. The parameter rm2(overall) penalizes a model for large differences between observed and predicted values of the compounds of the whole set (considering both training and test sets) while the parameter Rp2 penalizes model R2 for large differences between determination coefficient of nonrandom model and square of mean correlation coefficient of random models in case of a randomization test. Two other variants of rm2 parameter, rm2(LOO) and rm2(test), penalize a model more strictly than Q2 and R2pred respectively. Three different data sets of moderate to large size have been used to develop multiple models in order to indicate the suitability of the novel parameters in QSAR studies. The results show that in many cases the developed models could satisfy the requirements of conventional parameters (Q2 and R2pred) but fail to achieve the required values for the novel parameters rm2 and Rp2. Moreover, these parameters also help in identifying the best models from among a set of comparable models. Thus, a test for these two parameters is suggested to be a more stringent requirement than the traditional validation parameters to decide acceptability of a predictive QSAR model, especially when a regulatory decision is involved. Full article
(This article belongs to the Special Issue Molecular Diversity Feature Papers)

Review

Jump to: Research

Open AccessReview QSAR Models for Reproductive Toxicity and Endocrine Disruption Activity
Molecules 2010, 15(3), 1987-1999; doi:10.3390/molecules15031987
Received: 21 December 2009 / Revised: 29 January 2010 / Accepted: 19 March 2010 / Published: 22 March 2010
Cited by 15 | PDF Full-text (285 KB)
Abstract
Reproductive toxicity is an important regulatory endpoint, which is required in registration procedures of chemicals used for different purposes (for example pesticides). The in vivo tests are expensive, time consuming and require large numbers of animals, which must be sacrificed. Therefore an effort
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Reproductive toxicity is an important regulatory endpoint, which is required in registration procedures of chemicals used for different purposes (for example pesticides). The in vivo tests are expensive, time consuming and require large numbers of animals, which must be sacrificed. Therefore an effort is ongoing to develop alternative In vitro and in silico methods to evaluate reproductive toxicity. In this review we describe some modeling approaches. In the first example we describe the CAESAR model for prediction of reproductive toxicity; the second example shows a classification model for endocrine disruption potential based on counter propagation artificial neural networks; the third example shows a modeling of relative binding affinity to rat estrogen receptor, and the fourth one shows a receptor dependent modeling experiment. Full article
(This article belongs to the Special Issue Molecular Diversity Feature Papers)
Open AccessReview Simple Sequence Repeat Polymorphisms (SSRPs) for Evaluation of Molecular Diversity and Germplasm Classification of Minor Crops
Molecules 2009, 14(11), 4546-4569; doi:10.3390/molecules14114546
Received: 13 September 2009 / Revised: 5 November 2009 / Accepted: 10 November 2009 / Published: 10 November 2009
Cited by 59 | PDF Full-text (406 KB)
Abstract
Evaluation of the genetic diversity among populations is an essential prerequisite for the preservation of endangered species. Thousands of new accessions are introduced into germplasm institutes each year, thereby necessitating assessment of their molecular diversity before elimination of the redundant genotypes. Of the
[...] Read more.
Evaluation of the genetic diversity among populations is an essential prerequisite for the preservation of endangered species. Thousands of new accessions are introduced into germplasm institutes each year, thereby necessitating assessment of their molecular diversity before elimination of the redundant genotypes. Of the protocols that facilitate the assessment of molecular diversity, SSRPs (simple sequence repeat polymorphisms) or microsatellite variation is the preferred system since it detects a large number of DNA polymorphisms with relatively simple technical complexity. The paucity of information on DNA sequences has limited their widespread utilization in the assessment of genetic diversity of minor or neglected crop species. However, recent advancements in DNA sequencing and PCR technologies in conjunction with sophisticated computer software have facilitated the development of SSRP markers in minor crops. This review examines the development and molecular nature of SSR markers, and their utilization in many aspects of plant genetics and ecology. Full article
(This article belongs to the Special Issue Molecular Diversity Feature Papers)

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