G-protein coupled receptors: SAR analyses of neurotransmitters and antagonists.

BACKGROUND: From the deductive point of view, neurotransmitter receptors can be divided into categories such as cholinergic (muscarinic, nicotinic), adrenergic (alpha- and beta-), dopaminergic, serotoninergic (5-HT1 approximately 5-HT5), and histaminergic (H1 and H2). Selective agonists and antagonists of each receptor subtype can have specific useful therapeutic applications. For understanding the molecular mechanisms of action, an inductive method of analysis is useful. OBJECTIVE: The aim of the present study is to examine the structure-activity relationships of agents acting on G-protein coupled receptors. METHOD: Representative sets of G-PCR agonists and antagonists were identified from the literature and Medline [P.M. Walsh (2003) Physicians' Desk Reference; M.J. O'Neil (2001) The Merck Index]. The molecular weight (MW), calculated logarithm of octanol/water partition coefficient (C log P) and molar refraction (CMR), dipole moment (DM), E(lumo) (the energy of the lowest unoccupied molecular orbital, a measure of the electron affinity of a molecule and its reactivity as an electrophile), E(homo) (the energy of the highest occupied molecular orbital, related to the ionization potential of a molecule, and its reactivity as a nucleophile), and the total number of hydrogen bonds (H(b)) (donors and receptors), were chosen as molecular descriptors for SAR analyses. RESULTS: The data suggest that not only do neurotransmitters share common structural features but their receptors belong to the same ensemble of G-protein coupled receptor with seven to eight transmembrane domains with their resultant dipoles in an antiparallel configuration. Moreover, the analysis indicates that the receptor exists in a dynamic equilibrium between the closed state and the open state. The energy needed to open the closed state is provided by the hydrolysis of GTP. A composite 3-D parameter frame setting of all the neurotransmitter agonists and antagonists are presented using MW, Hb and mu as independent variables. CONCLUSION: It appears that all neurotransmitters examined in this study operate by a similar mechanism with the G-protein coupled receptors.

Structure-activity relationship: analyses of p-glycoprotein substrates and inhibitors.

OBJECTIVE: A large number of structurally and functionally diverse compounds act as substrates or modulators of p-glycoprotein (p-gp). Some of them possess multiple drug resistance (MDR)-reversing activity, but only a small number of them have entered clinical study. In order to uncover the factors which exert a significant impact on the interaction between substrates/modulators and p-gp, we have performed structure-activity relationship (SAR) analyses, including molecular modelling, two-dimensional (2D) and three-dimensional (3D) parameter-frame-setting analysis, quantitative structure activity relationship (QSAR) analysis among substrates/modulators, as well as clinically promising MDR-reversing agents. METHODS: The physicochemical parameters C log P, CMR and all regression equations were derived by using C log P version 4.0 and the latest CQSAR software, respectively. Molecular modelling and all other parameter calculations were performed by using HyperChem version 5.0 program, after geometry optimization and energy minimization using the AM1 semiempirical method. RESULTS: SAR analyses indicate that MDR reversal activity is correlated with the lipophilicity (C log P), molecular weight (log Mw), longest chain (Nlc) of the molecule and the energy of the highest occupied orbital (Ehomo). In addition, the presence of a basic tertiary nitrogen atom in the structure is also an important contributor to p-gp inhibitory activity. Some separation in space is achieved for different subsets of p-gp substrates and inhibitors using Nlc, C log P and Ehomo as three independent parameters in the 3D-parameter-frame setting. CONCLUSION: A highly effective p-gp modulator candidate should possess a log P value of 2.92 or higher, 18-atom-long or longer molecular axis, and a high Ehomo value, as well as at least one tertiary basic nitrogen atom. The results obtained may be useful in explaining drug-p-gp interactions for different compounds, including drug interactions and the development of new MDR chemosensitizers.

Development of HIV protease inhibitors: a survey.

In the treatment of infections caused by rapidly mutating viruses like human immunodeficiency virus (HIV), combination therapy with multiple drugs acting by different mechanisms offers several advantages over monotherapy. It may provide: synergistic effect, possible reduction of dosages and side-effects, and reduction of the chance of drug resistance. In the past few years, hundreds of HIV protease inhibitors have been synthesized and tested in order to overcome the limitations of reverse transcriptase inhibitors like zidovudine and others. In this review, emphasis is placed on the development of HIV protease inhibitors as antiviral agents against HIV, and structure-activity relationship analysis of saquinavir and related compounds. Limitations of some protease inhibitors and ways to overcome the shortcomings are presented. Among these many protease inhibitors five have been marketed during 1995-1999. They are saquinavir, ritonavir, indinavir, nelfinavir and amprenavir. Their different structural features, important physicochemical, pharmacokinetic and clinical profiles are presented in a table form for easy comparison. It is hoped that in the future new drugs based on additional mechanisms can be developed for the treatment of AIDS.

Purine analogs as CDK enzyme inhibitory agents: a survey and QSAR analysis.

Characterization of the cell cycle has introduced CDKs and other proteins as possible targets for inhibition of cell proliferation, such as, CDK1 and CDK2, whose inhibition may be useful in the treatment of proliferative disorders. Structure-activity analyses have been instrumental in the design and discovery of potent CDK inhibitors, such as purine analogs, which have increased in potency from the micromolar to the nanomolar level. X-ray crystallography and molecular modeling have provided evidence that these compounds act on the CDK target enzyme. Selected CDK inhibitors have successfully entered clinical trials. Further characterization of the cell cycle to identify molecular targets to inhibit cell proliferation, QSAR and SAR studies, and clinical trials may expedite the development of CDK inhibitors for therapeutic use. The ultimate goal of these studies is to determine whether specific CDKs, CDK1 or CDK2, are enzymes essential to cell proliferation that can be targeted for treatment of proliferative disorders. CDK1 and CDK2 are viable molecular targets for cancer therapies based on isolated-enzyme inhibition by CDK inhibitors, successful clinical trials of CDK1 and CDK2 inhibitors, and x-ray crystallographic confirmation of CDK inhibitors binding to the putative target enzyme active site. It is now reported that CDK1 inhibitory activities of purine analogs correlate with the physiochemical parameters of purine analogs. Enzyme inhibition [1-5], clinical trials (see Tab. 1), x-ray crystallographic [4, 6, 7] and QSAR correlation studies are evidence that specific CDK1 and/or CDK2 inhibitors are potentially useful agents for various cell-proliferation disorders. A brief overview of the cell cycle precedes a literature review of clinical applications of CDK inhibitors, followed by a new QSAR study, and a SAR and molecular modeling discussion.

Inhibition of tumor cell growth by Schiff bases of hydroxysemicarbazide.

The inhibitory activities of Schiff bases of hydroxysemicarbazide (HSC) against eight human and murine tumor cell lines and one non-cancer cell line were studied using MTS/PES microculture tetrazolium and methylene blue assays. Compounds 1 (1-[9-(10-methylanthryl)methylene]-4-HSC), 2 (1-[2-hydroxy-3,5-dibromobenzylidene]-4-HSC) and 3 (1-[2,3,4-trihydroxybenzylidene]-4-HSC), which have been shown to be active against murine leukemia L1210 cells in our laboratories, inhibited human leukemia CCRF-CEM cells with similar IC50s ranging from 2.7 to 7.0 microM. Of the compounds tested against attached tumor cell lines (B16, CHO, HT29, ZR75) at 50 microM concentration, compound 1 showed the strongest inhibition, followed by 4 (1-[2-(5-nitrothienyl)methylene]-4-HSC), 2 and 5 (1-[2-hydroxy-3,5-diiodobenzylidene]-4-HSC) with more than 50% inhibition. The IC50s of compound 1 were found to range from 2.7 to 12 microM against the attached tumor cell lines examined. As compared with hydroxyurea, compound 1 had more favorable selectivity against tumor cells. Further more, compound 1 was found to have IC50s of 2.8 and 6.5 microM against hydroxyurea-resistant and gemcitabine-resistant KB cells, respectively, but had no cross-resistance with hydroxyurea and gemcitabine (two known ribonucleotide reductase inhibitors acting at different sites of the same enzyme). In conclusion, several Schiff bases of HSC showed inhibition of tumor cell growth at micromolar concentration and had no cross-resistance with hydroxyurea-resistant KB cells.

Glucosamine and chondroitin sulfates in the treatment of osteoarthritis: a survey.

For more than 30 years, non-steroidal anti-inflammatory drugs (NSAIDs) have been used as standards in the treatment of osteoarthritis (OA). Serious and often life-threatening adverse effects due to these agents are common. Clinical findings have revealed that glucosamine sulfate and chondroitin sulfate are effective and safer alternatives to alleviate symptoms of OA. Experimental evidence indicates that these compounds and their low molecular weight derivatives have a particular tropism for cartilage where they serve as substrates in the biosynthesis of component building blocks. This paper is a literature review of the chemistry, mechanism of action, pharmacokinetics, clinical efficacy and safety of these two nutraceuticals.

Caco-2 cell permeability vs human gastrointestinal absorption: QSPR analysis.

The aim of this study is to elucidate quantitative structure-permeability relationship (QSPR) of various organic molecules through Caco-2 cells, and to ascertain the relationship between gastrointestinal (GI) absorption in humans and Caco-2 cell permeability. Caco-2 cell permeability and human GI absorption data were obtained from the literature. The maximum hydrogen bond-forming capacity corrected for intra-molecular H-bonding (Hbc) and Lien's QSAR model were used in this study. The latest CQSAR software was utilized in calculating the logarithm of partition coefficient in octanol/water (Clog P) and in deriving all regression equations. For 51 compounds, a significant correlation was obtained between Caco-2 cell permeability (log Pcaco-2) and Hbc, octanol/PBS (phosphate buffered saline, pH 7.4) distribution coefficient (log Doct), log MW and an indicator variable (I) for the charge, with a correlation coefficient of 0.797. When these compounds were divided into three subgroups, namely neutral, cationic and anionic compounds, much better correlations (r = 0.968, 0.915 and 0.931, respectively) were obtained using different combinations of various physico-chemical parameters. A plot of human GI absorption vs. Caco-2 cell permeability obtained from different laboratories reveals that Caco-2 cell permeability cannot be used to precisely predict human GI absorption for compounds with Pcaco-2 below 5 x 10(-6) cm/s, due to interlaboratory and experimental variabilities, and the lack of a simple correlation between human GI absorption and Caco-2 cell permeability. Caco-2 cell permeability may be estimated from the structures of drug molecules using the above-mentioned physicochemical parameters. In general, for compounds with Pcaco-2 above 5 x 10(-6) cm/s, human GI absorption ranges from 50 to 100%. This is generally acceptable for development into oral dosage form. For the compounds with Pcaco-2 below 5 x 10(-6) cm/s, careful interpretation of caco-2 cell permeability and use of internal standard for comparison are recommended. Otherwise, good drug candidates may be excluded due to incorrectly predicted poor absorption.

Inhibition of ribonucleotide reductase by a new class of isoindole derivatives: drug synergism with cytarabine (Ara-C) and induction of cellular apoptosis.

The hydroxyisoindole dione derivatives ISID and MISID are new compounds with structures resembling purines and possessing a hydroxamic acid moiety which is the pharmacophore of hydroxyurea (HU), an inhibitor of ribonucleotide reductase (RR). ISID and MISID exhibited 100- to 500-fold higher cytotoxicity as compared to HU against cell lines sensitive (CEM/0) or resistant to ara-C (CEM/ara-C/7A; CEM/dCk[-]). Both MISID and ISID showed significant inhibitory activity of ribonucleotide reductase (RR). Treatment of CEM/0 cells with 10 microM ISID showed a linear decrease in all the dNTPs leading to a complete depletion by 4 hours with no recovery of enzymatic activity of RR up to 48 hours in the presence of the drug, suggesting an irreversible inhibition of this enzyme. However, 10 microM MISID caused a significant time dependent, but reversible inhibition of RR in a whole cell assay in CEM/0 cells. Pretreatment of CEM/0 cells with 10 microM MISID for 1 hour increased cellular ara-CTP concentrations approximately 2-fold as compared to untreated controls. However, a reduction in intracellular ara-CTP concentration was observed following a commensurate depletion of ATP in these cells after 4 hrs of ISID pretreatment. Similarly, the ara-CTP concentration was augmented by 1.6-fold following pretreatment of CEM/0 cells with 10 microM MISID for 4 hours. Significant apoptotic cell death was detected in CEM/0 cells treated with ara-C, ISID or MISID alone or in combination. Ara-C treatment induced HMW (high molecular weight) DNA fragmentation at earlier times which subsequently led to oligonucleosomal DNA fragmentation by 48 hrs. The sequential treatment of CEM/0 cells with MISID followed by ara-C resulted in increased DNA fragmentation in the 2.0 to 4.0 Kb range in comparison to those cells treated with either ara-C or MISID alone. The increased apoptotic cell death explained the synergistic cytotoxicity of the combination of ara-C and MISID against CEM/0 cells observed earlier. We conclude that the inhibition of RR by these agents induces leukemic cell apoptosis, a mechanism which is further potentiated when these RR inhibitors are combined with ara-C. Since new compounds do not require activation, as do other clinically useful RR inhibitors, further studies for their potential use against leukemias and solid tumors are warranted.

Antiviral tannins from two Phyllanthus species.

Seven ellagitannins isolated from Phyllanthus myrtifolius and P. urinaria (Euphorbiaceae) have been shown, for the first time, to be active against Epstein-Barr virus DNA polymerase (EBV-DP) at the microM level. All these compounds have the same moiety of a corilagin, and differ from each other by different substitutions at C-2 and C-4 of the glucose core. SAR analysis and molecular modeling reveal that the essential pharmacophore of these tannins resides in the corilagin moiety. The outer complex carboxylic acid moieties appear to act only as auxopharmacore.

Quantitative structure-activity relationship analysis of phenolic antioxidants.

In this report, the quantitative structure-activity relationship (QSAR) analyses of substituted phenols, vitamin E derivatives and flavonoids are presented. Two models have been derived using calculated parameters such as the heat of formation (Hf), the energy of the lowest unoccupied molecular orbital of radicals (E(lumo-r)) the energy of the highest occupied molecular orbital of the parent compounds (E(homo)) and the number of hydroxyl groups (OH). These models can be used to estimate the redox potentials or antioxidant activities of new substituted phenolic compounds or vitamin E derivatives. The Trolox equivalent antioxidant capacities (TEACs) of 42 different flavonoids are found to be mainly governed by the number and location of hydroxyl groups on the flavonoid ring system.

Inhibition of herpes simplex virus type 1 and adenovirus type 5 by heterocyclic Schiff bases of aminohydroxyguanidine tosylate.

Eleven heterocyclic Schiff bases of aminohydroxyguanidine tosylate (SB-AHGs), compounds I-XI, were tested for antiviral activity against herpes simplex virus type 1 (HSV-1) and adenovirus type 5 (Ad 5) via plaque reduction and virus yield reduction assays. This work was undertaken to test the hypothesis that low molecular weight SB-AHGs (MW < 235 for the free SB) make better antiviral agents than high MW SB-AHGs (MW > 300). The plaque reduction assay method demonstrated that three compounds, I, VII and IX, had moderate activity against HSV-1, with 50% inhibitory concentration (IC50) values of 38.0, 23.5 and 52.1 microM, respectively. Against Ad 5, compounds I, VIII and XI exhibited moderate activity, with IC50 values of 52.7, 19.3 and 5.1 microM, respectively. Among the compounds screened, compound I (1-[(3'-hydroxy-6'-methyl-2'-pyridyl)methylene]amino-3-hydroxyguanidi ne tosylate) was the most promising antiviral candidate, with selectivity indices (SI) of 10.2 (HSV-1) and 7.6 (Ad 5), respectively. Virus yield reduction assays indicated that compound I had less antiviral potency against HSV-1 than against Ad 5. The antiviral effects of compound I at a high input virus multiplicity of infection (MOI > 5) indicated that compound I had effective anti-adenoviral activity at 24 h post infection. This work demonstrated that some of SB-AHGs only have moderate antiviral activities against Ad 5 and HSV-1 viruses. In general, low MW SB-AHGs have low cytotoxicities to the host cells.

QSAR analysis of polyamine transport inhibitors in L1210 cells.

PURPOSE: In this paper, the authors attempt to construct a mathematical model to correlate the biological activities of 63 polyamine transport inhibitors in L1210 cells with their physicochemical parameters. METHOD: The inhibitory constants (Ki) were obtained from the published work of Bergeron et al. Non-weighted least square method was used in deriving the regression equations with a BMDP program. An AM1 subroutine of the HyperChem program was used to optimize the geometry and calculate the molecular dipole moments and the distance between two terminal amino groups. A CQSAR program was used to calculate Clog P (oct./w.). RESULTS: A good correlation (r2 = 0.81) was obtained by using a five-parameter equation including the distance between two terminal amino groups (d), the number of cationic charge (Charge), molecular weight (MW), dipole moment (mu), and hydrogen bond forming ability (Hb). CONCLUSION: This model accounts for 81% of the variance in the data and can be used to estimate transport-inhibitory activity of many other polyamine analogues. It gives some quantitative information about the relationship between the polyamine analogues' function as transport inhibitors and their molecular structures.

Dihydroorotate dehydrogenase inhibitors: quantitative structure-activity relationship analysis.

PURPOSE: The main purpose of this study is to analyze the quantitative structure-activity relationship of two series of dihydroorotate dehydrogenase inhibitors (leflunomide and quinoline carboxylic acid analogues), and to determine the structural requirements for optimum activity of these analogues. METHODS: A new CQSAR program was used in deriving regression equations and calculating the octanol/water partition coefficient and the molar refractivity values. The molecular modeling was performed using the HyperChem program. RESULTS: Statistically significant correlations were obtained using a combination of 3-4 parameters. The structural requirements for optimum activity and critical regions for the inhibitory activity of dihydroorotate dehydrogenase were identified. CONCLUSIONS: The quantitative structure-activity relationship analysis demonstrated that two series of dihydroorotate dehydrogenase inhibitors may bind to different binding sites on the enzyme. These results provide a better understanding of dihydroorotate dehydrogenase inhibitor-enzyme interactions, and may be useful for further modification and improvement of inhibitors of this important enzyme.

Development of HIV protease inhibitors: a survey.

In the treatment of infections caused by rapidly mutating viruses like human immunodeficiency virus (HIV), combination therapy with multiple drugs acting by different mechanisms offers several advantages over monotherapy. It may provide: synergistic effect, possible reduction of dosages and side-effects, and reduction of the chance of drug resistance. In the past few years, hundreds of HIV protease inhibitors have been synthesized and tested in order to overcome the limitations of reverse transcriptase inhibitors like zidovudine and others. In this review, emphasis is placed on the development of HIV protease inhibitors as antiviral agents against HIV, and structure-activity relationship analysis of saquinavir and related compounds. Limitations of some protease inhibitors and ways to overcome the shortcomings are presented. Among these many protease inhibitors four have been marketed during 1995-1997. They are saquinavir, ritonavir, indinavir and nelfinavir. Their different structural features, important physicochemical, pharmacokinetic and clinical profiles are presented in a table form for easy comparison. It is hoped that in the future new drugs based on additional mechanisms can be developed for the treatment of AIDS.

Physicochemical basis of the universal genetic codes--quantitative analysis.

Quantitative mathematic models have been developed to correlate the fragment hydrophobicity contribution constants (faa) of 20 amino acids with the physicochemical properties (mu, Hb, and square root of MW) of the four bases (U, A, C, G) of the codons, or those of the anticodons. Using the general equation faa = a mu 1 + b mu 2 + c mu 3 + d square root of MW1 + e square root of MW2 + f square root of MW3 + g Hb1 + h Hb2 + i Hb3 + j, where 1, 2, 3 refer to the first, the second and the third base respectively, correlation coefficient of about 0.82 can be obtained for all 20 amino acids coded by 61 different triplet codes. These correlations are statistically highly significant, even though they do not take into account the involvement of various factors and peptidyl transferases. Furthermore, the reasons for the three stop codons are revealed. The graphic presentation of the codons and the amino acids coded separates the acidic and the basic, the aromatic and the heterocyclic amino acids into different quadrants of an octagon. This is in agreement with the ancient Chinese Ying-Yang theory embedded in the classical I-Ching.

Natural products and their derivatives as cancer chemopreventive agents.

This review summarizes currently available data on the chemopreventive efficacies, proposed mechanisms of action and relationships between activities and structures of natural products like vitamin D, calcium, dehydroepidandrosterone, coenzyme Q10, celery seed oil, parsley leaf oil, sulforaphane, isoflavonoids, lignans, protease inhibitors, tea polyphenols, curcumin, and polysaccharides from Acanthopanax genus.

Correlation of physiochemical parameters to the hydrophobic contribution constants of amino acid residues in small peptides.

PURPOSE: This paper attempts to correlate the hydrophobic contribution constants (faa) of 21 amino acids in small peptides with commonly used physiochemical parameters. These faa constants can then be used to predict hydrophobicity change in peptides when any one of the amino acid residue is substituted with another. METHOD: Non-weighted least squares method was used in deriving regression equations with a BMDP program. A Hyperchem program for Windows was used to calculate the group dipole moments of the side chain. RESULTS: A good correlation (r = 0.97) was obtained using a four parameter equation including molecular weight (log MW), hydrogen bond forming ability (HB), dipole moment (mu) and an indicator variable (I) to account for the presence of a free primary amine group in the side chain. CONCLUSIONS: This proposed model should be useful in predicting the hydrophobic contribution constants of other uncommon amino acids and in the estimation of log P'values of numerous peptides containing different possible combinations of these amino acids, as well as log P' values resulting from amino acid substitution as is done in site-directed mutagenesis.

Immunostimulating polysaccharides from Panax notoginseng.

PURPOSE: The main purpose of this study is to prepare and characterize polysaccharides from Panax notoginseng, investigate their effects on immune system in vitro in order to find new immunostimulants for the prevention and supporting treatment of infection and immunodeficiency related diseases. METHODS: Polysaccharides were extracted with aqueous solution, separated with column chromatography. Their anticomplementary activities were investigated by using human serum and antibody-sensitized sheep red blood cells. Interferon-gamma and tumor necrosis factor inductive activities were studied by using isolated mouse spleen lymphocytes and peritoneal macrophages, respectively. RESULTS: Four polysaccharides, homogeneous in gel-filtration chromatography, were prepared and designated PF3111, PF3112, PBGA11, and PBGA12. Component sugar analysis revealed that they are heteroglycans with MWs ranging from 37 kD to 760 kD, composed of glucose, galactose, arabinose, mannose, and xylose in different molar ratios. Fraction PBGA12 has the most anticomplementary activity which is mediated through both alternative and classical pathways. All the polysaccharides except PBGA11 induced the production of interferon-gamma in the presence of concanavalin A. They induced the production of significant amount of TNF-alpha in cell cultures. CONCLUSIONS: The polysaccharides from P.notoginseng have immunostimulating activities in vitro.

Hormone therapy and phytoestrogens.

As ageing progresses the levels of sex hormones decrease in the human body. In the male population, the decrease or absence of testosterone leads to decreased strength and stamina, thin bones and a low sex drive (1). In the female population, the immediate symptoms of menopause include irregular periods, painful sexual intercourse due to vaginal dryness, hot flushes and night sweats (2). Lack of oestrogen also leads to the risk of developing osteoporosis and cardiovascular diseases. In this report, the authors will mainly discuss the effects of hormone therapy (HT) in menopausal women. Available current clinical data on the effects of calcium supplementation with and without HT, exercise, exercise plus calcium and exercise with HT on bone loss are presented. The effects of transdermal and oral oestrogen therapy (OT) on serum lipids are discussed. Commercially-available HT products, their indications, dosages, contra-indications, side-effects and drug interactions are compared. Alternative therapies for menopausal symptoms with Chinese traditional herbs, and a comparison of the molecular structures of phytoestrogens with estradiol and diethylstilbestrol are examined (3, 4). A list of medicinal herbs and foods reported to elicit an oestrogenic response in animals is compiled.

QSAR analysis of membrane permeability to organic compounds.

A general mathematical model involving partition coefficient, molecular weight and hydrogen bonding is used to correlate the structures and permeability of various organic compounds through the toad urinary bladder and human red blood cell (RBC) membranes. Log Per (permeability) is correlated with log Po/w (partition coefficient in olive oil/water, or ether/water), log MW (molecular weight) and Hb (hydrogen bonds). Log Po/w is the most important factor among three parameters examined. While increased MW always has a negative effect on the permeability, increased Hb can have either a slightly positive or a slightly negative effect depending on the solvent and membrane systems used. Systematic comparison of the QSAR's (quantitative structure activity relationship) of different biological membranes may serve as a useful guide in drug targeting to different tissues and cell types.