Selection for variables in quantitative structure-activity/property relationship studies - Comparison between methods of orthogonal descriptors and leaps-and-bounds regression analysis

In this paper, the comparison of orthogonal descriptors and Leaps-and-Bounds regression analysis is performed. The results obtained by using orthogonal descriptors are better than that obtained by using Leaps-and-Bounds regression for the data set of nitrobenzenes used in this study. Leaps-and-Bounds regression can be used effectively for selection of variables in quantitative structure-activity/property relationship(QSAR/QSPR) studies. Consequently, orthogonalisation of descriptors is also a good method for variable selection for studies on QSAR/QSPR.

QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS FOR TOXICITY OF PHENOLS USING REGRESSION-ANALYSIS AND COMPUTATIONAL NEURAL NETWORKS

Quantitative structure-toxicity models were developed that directly link the molecular structures of a et of 50 alkYlated and/or halogenated phenols with their polar narcosis toxicity, expressed as the negative logarithm of the IGC50 (50% growth inhibitor

Molecular Modeling and Affinity Determination of scFv Antibody: Proper Linker Peptide Enhances Its Activity

One of existing strategies to engineer active antibody is to link VH and VL domains via a linker peptide. How the composition, length, and conformation of the linker affect antibody activity, however, remains poorly understood. In this study, a dual approach that coordinates molecule modeling, biological measurements, and affinity evaluation was developed to quantify the binding activity of a novel stable miniaturized anti-CD20 antibody or singlechain fragment variable (scFv) with a linker peptide. Upon computer-guided homology modeling, distance geometry analysis, and molecular superimposition and optimization, three new linker peptides PT1, PT2, and PT3 with respective 7, 10, and 15 residues were proposed and three engineered antibodies were then constructed by linking the cloned VH and VL domains and fusing to a derivative of human IgG1. The binding stability and activity of scFv-Fc chimera to CD20 antigen was quantified using a micropipette adhesion frequency assay and a Scatchard analysis. Our data indicated that the binding affinity was similar for the chimera with PT2 or PT3 and ~24-fold higher than that for the chimera with PT1, supporting theoretical predictions in molecular modeling. These results further the understanding in the impact of linker peptide on antibody structure and activity.

A novel heme-containing protein with anti-HIV-1 activity from skin secretions of Bufo andrewsi

A novel protein, named BAS-AH, was purified and characterized from the skin of the toad Bufo andrewsi. BAS-AH is a single chain protein and the apparent molecular weight is about 63 kDa as judged by SDS-PAGE. BAS-AH was determined to bind heme (0.89 mol heme/mol protein) as determined by pyridine haemochrome analysis. Fifty percentage cytotoxic concentration (CC50) of BAS-AH on C8166 cells was 9.5 mu M. However, at concentrations that showed little effect oil cell viability, BAS-AH displayed dose dependent inhibition oil HIV-1 infection and replication. The antiviral selectivity indexes corresponding to the measurements of syncytium formation and HIV-1 p24 (CC50/EC50) were 14.4 and 11.4, respectively, corresponding to the . BAS-AH also showed an inhibitory effect on the activity of recombinant HIV-1 reverse transcriptase (IC50 = 1.32 mu M). The N-terminal sequence of BAS-AH was determined to be NAKXKADVIGKISILLGQDNLSNIVAM, which exhibited little identity with other known anti-HIV-1 proteins. BAS-AH is devoid of antibacterial, protcolytic, trypsin inhibitory activity, (L)-amino acid oxidase activity and catalase activity. (c) 2005 Elsevier Ltd. All rights reserved.

A serine proteinase inhibitor from frog eggs with bacteriostatic activity

By Sephadex G-50 gel filtration, Resource Q anionic exchange and C4 reversed phase liquid high performance liquid chromatography, a proteinase inhibitor protein (Ranaserpin) was identified and purified from the eggs of the odour frog, Rana grahami. The protein displayed a single band adjacent to the molecular weight marker of 14.4 kDa analyzed by SDS-PAGE. The inhibitor protein homogeneity and its molecular weight were confirmed again by MALDI-TOF mass spectrometry analysis. The MALDI-TOF mass spectrum analysis gave this inhibitor protein an m/z of 14422.26 that was matched well with the result from SDS-PAGE. This protein is a serine proteinase inhibitor targeting multiple proteinases including trypsin, elastase, and subtilisin. Ranaserpin inhibited the proteolytic activities of trypsin, elastase, and subtilisin. It has an inhibitory constant (K-i) of 6.2 x 10(-8) M, 2.7 x 10(-7) M and 2.2 x 10(-8) M for trypsin, elastase, and subtilisin, respectively. This serine proteinase inhibitor exhibited bacteriostatic effect on Gram-positive bacteria Bacillus subtilis (ATCC 6633). It was suggested that ranaserpin might act as a defensive role in resistance to invasion of pests or pathogens. This is the first report of serine proteinase inhibitor and its direct defensive role from amphibian eggs. (C) 2007 Elsevier Inc. All rights reserved.

Toward an understanding of the molecular mechanism for successful blood feeding by coupling proteomics analysis with pharmacological testing of horsefly salivary glands

Horseflies are economically important blood-feeding arthropods and also a nuisance for humans and vectors for filariasis. They rely heavily on the pharmacological properties of their saliva to get a blood meal and suppress immune reactions of hosts. Little information is available on antihemostatic substances in horsefly salivary glands; especially no horsefly immune suppressants have been reported. By proteomics or peptidomics and coupling transcriptome analysis with pharmacological testing, several families of proteins or peptides, which act mainly on the hemostatic system or immune system of the host, were identified and characterized from 30,000 pairs salivary glands of the horsefly Tabanus yao (Diptera, Tabanidae). They are: (i) a novel family of inhibitors of platelet aggregation including two members, which possibly inhibit platelet aggregation by a novel mechanism and act on platelet membrane, (ii) a novel family of immunosuppressant peptides including 12 members, which can inhibit interferon-gamma production and increase interleukin-10 secretion, (iii) a serine protease inhibitor with 56 amino acid residues containing anticoagulant activity, (iv) a serine protease with anticoagulant activity, (v) a protease with fibrinogenolytic activity, (vi) three families of antimicrobial peptides including six members, (vii) a hyaluronidase, (viii) a vasodilator peptide, which is an isoform of vasotab identified from Hybomitra bimaculata, and interestingly (ix) two metallothioneins, which are the first metallothioneins reported from invertebrate salivary glands. The current work will facilitate the understanding of the molecular mechanisms of the ectoparasite-host relationship and help in identifying novel vaccine targets and novel leading pharmacological compounds.

Purification and cloning of a novel C-type lectin-like protein with platelet aggregation activity from Trimeresurus mucrosquamatus venom

TMVA, a novel C-type lectin-like protein that induces platelet aggregation in a dose-dependent manner, was purified from the venom of Trimeresurus mucrosquamatus. It consists of two subunits, alpha (15,536 Da) and beta (14,873 Da). The mature amino acid sequences of the a (135 amino acids) and beta subunits (123 amino acids) were deduced from cloned cDNAs. Both of the sequences show great similarity to C-type lectin-like venom proteins, including a carbohydrate recognition domain. The cysteine residues of TMVA are conserved at positions corresponding to those of flavocetin-A and convulxin, including the additional Cys135 in the alpha subunit and Cys3 in the beta subunit. SDS-PAGE, mass spectrometry analysis and amino acid sequence showed that native TMVA exists as two convertible multimers Of (alphabeta)(2) and (alphabeta)(4) with molecular weights of 63,680 and 128,518 Da, respectively. The (alphabeta)(2) complex is stabilized by an interchain disulfide bridge between the two alphabeta-heterodimers, whereas the stabilization of the (alphabeta)(4) complex seems to involve non-covalent interactions between the (alphabeta)(2) complexes. (C) 2002 Elsevier Science Ltd. All rights reserved.

Lancifodilactone G: A unique nortriterpenoid isolated from Schisandra lancifolia and its anti-HIV activity

Lancifodilactone G (1), a novel, highly oxygenated nortriterpenoid featuring a partial enol structure and a spirocyclic moiety, was isolated from the medicinal plant Schisandra lancifolia. Its structure and stereochemistry were determined from extensive one- and two-dimensional NMR and mass spectral data, coupled with single-crystal X-ray analysis. Compound 1 exerted minimal cytotoxicity against C8166 cells (CC50 > 200 mu g/mL) and showed anti-HIV activity with EC50 = 95.47 +/- 14.19 mu g/mL and a selectivity index in the range of 1.82-2.46.

Lancifodilactone F: A novel nortriterpenoid possessing a unique skeleton from Schisandra lancifolia and its anti-HIV activity

Lancifodilactone F (1), possessing an unprecedented rearranged pentanortriterpenoid backbone derived from cycloartane, was isolated from the leaves and stems of Schisandra lancifolia (Rehd. et Wils) A. C. Smith. Its structure was established by comprehensive NMR and MS spectroscopic analysis, coupled with single-crystal X-ray experiment. Compound 1 exerted minimal cytotoxicity against C8166 cells (CC50 > 200 mu g/mL) and showed anti-HIV activity with EC50 = 20.69 +/- 3.31 mu g/mL and a selectivity index > 6.62.

Octanorcucurbitane and cucurbitane triterpenoids from the tubers of Hemsleya endecaphylla with HIV-1 inhibitory activity

Two new cucurbitacins, endecaphyllacins A (1) and B (2), together with six known analogues (3-8), were isolated from the tubers of Hemsleya endecaphylla. The structures of 1 and 2 were elucidated by NMR and MS spectroscopic analysis. The relative stereoch

Synthesis and Anti-Human Immunodeficiency Virus Type 1 Activity of (E)-N-Phenylstyryl-N-alkylacetamide Derivatives

A series of (E)-N-phenylstyryl-N-alkylacetamides, 5, were synthesized by direct reduction-acetylation of beta-arylnitroolefins, followed by N-alkylation. The title compounds were characterized by H-1-NMR, EIMS and IR analysis. All the synthesized compound

Antimicrobial activity-specific to Gram-negative bacteria and immune modulation-mediated NF-kappa B and Sp1 of a medaka beta-defensin

Defensins are a group of cationic antimicrobial peptides which play an important role in the innate immune system by exerting their antimicrobial activity against pathogens. In this study, we cloned a novel beta-defensin cDNA from medaka (Oryzias latipes) by rapid amplification of cDNA ends (RACE) technique. The full-length cDNA consists of 480 bp, and the open reading frame (CRF) of 189 bp encodes a polypeptide of 63 amino acids (aa) with a predicted molecular weight of 7.44 kDa. Its genomic organization was analyzed, and Southern blot detection confirmed that only one copy of beta-defensin exists in the medaka HNI strain. RT-PCR, Western blot and immunohistochemistry detections showed that the beta-defensin transcript and protein could be detected in eyes, liver, kidney, blood, spleen and gill, and obviously prevalent expression was found in eyes. Antimicrobial activity of the medaka beta-defensin was evaluated, and the antibacterial activity-specific to Gram-negative bacteria was revealed. Furthermore, the lipopolysaccharide (LPS), a major component of the outer membrane of Gram-negative bacteria, was demonstrated to be able to induce about 13-fol up-regulation of the beta-defensin within first 12 h. In addition, promoter and promoter mutagenesis analysis were performed in the medaka beta-defensin. A proximal 100 base pair(bp) sequence (+26 to -73)and the next 1700 bp sequence (-73 to -1755) were demonstrated to be responsible for the basal promoter activity and for the transcription regulation. Three nuclear factor kappa B (NF-kappa B) cis-elements and a Sp1 cis-element were revealed by mutagenesis analysis to exist in the 5' flanking sequence, and they were confirmed to be responsible for the up-regulation of medaka beta-defensin stimulated by LPS. And, the Sp1 cis-element was further revealed to be related to the basal promoter activity, and transcriptional factor II D (TFIID) was found to be in charge of the gene transcription initiation. All the obtained data suggested that the novel medaka beta-defensin should have antimicrobial activity-specific to Gram-negative bacteria, and the antibacterial immune function should be modulated by NF-kappa B and Sp1. (C) 2008 Elsevier Ltd. All rights reserved.