The RNA Polymerase Structure–Function Study (1962–2001)

The study of RNA polymerase initiated by R.B. Khesin has been conducted for about forty years at the laboratory founded by him (since 1989, in collaboration with A. Goldfarb's laboratory). Genetic methods are used in combination with methods of the specific chemical crosslinks of nucleic acids with proteins. The paper assesses the main results of the study in comparison with the recent high-resolution X-ray crystallographic data. A short comparative summary of the RNA polymerase structure is presented for bacteria, archaebacteria, and eukaryotic organelles and nuclei. A brief history of the RNA polymerase study is also given.     

Structure–Function Studies on Non-synonymous SNPs of Chemokine Receptor Gene Implicated in Cardiovascular Disease: A Computational Approach

Among non-communicable diseases, cardiovascular disease (CVD) is claimed to be the leading cause of death worldwide. The chemokine (C–C Motif) receptor 5 (CCR5) gene has a strong association with the development of CVD and may culminate in myocardial infarction. In this study, its potential variations have been determined using molecular dynamics approach. Single nucleotide polymorphisms (SNPs) are the predominant mutations and their deleterious effects were initially screened using prediction tools. Further, for the 75 % of deleterious non-synonymous SNPs predicted in common by the above tools, root mean square deviation (RMSD) and stability residues were determined using SWISS-PDB viewer and SRide server respectively. Accordingly, four point mutations L55Q, V131F, R223W, and G301R which had RMSD ≥2.0 Å were selected and trajectory analyses were performed. In common, all trajectory analyses reported no similarities between native and mutants. Combined mutational analysis comparing all the mutants together with the native also showed significant and similar changes. Thus we conclude that the above four mutations are the potential targets of CCR5 and may lead to CVD.     

Refinement of a Quantitative Structure–Activity Relationship Model for Prediction of Cell-Penetrating Peptide Based Transfection Systems

Cell-penetrating peptide (CPP) based transfection systems (PBTS) are a promising class of drug delivery vectors. CPPs are short mainly cationic peptides capable of delivering cell non-permeant cargo to the interior of the cell. Some CPPs have the ability to form non-covalent complexes with oligonucleotides for gene therapy applications. In this study, we use quantitative structure–activity relationships (QSAR) , a statistical method based on regression data analysis. Here, an fragment QSAR (FQSAR) model is developed to predict new peptides based on standard alpha helical conformers and Assisted Model Building with Energy Refinement molecular mechanics simulations of previous peptides. These new peptides were examined for plasmid transfection efficiency and compared with their predicted biological activity. The best predicted peptides were capable of achieving plasmid transfection with significant improvement compared to the previous generation of peptides. Our results demonstrate that FQSAR model refinement is an efficient method for optimizing PBTS for improved biological activity.     

Quantitative Structure–Activity Relationship Model for Prediction of Protein–Peptide Interaction Binding Affinities between Human Amphiphysin-1 SH3 Domains and Their Peptide Ligands

Protein–protein interaction plays a critical role in signal transduction and many other key biological processes. The present study evaluated four parameters selected from among 554 physiochemical variables of 20 natural amino acids listed in AAindex, namely, hydrophobicity, electronic properties, steric properties, and hydrogen-bond properties. Human amphiphysin-1 Src homology 3 (SH3) domain-binding decapeptides were the object of analysis. A quantitative structure–activity relationship model of the SH3 domain-binding peptides was constructed using multivariate linear regression. The results showed that the four parameters ably characterize the structure of SH3 domain-binding decapeptides, have definitive physicochemical properties and a low level of computational complexity, are accessible, and may be used in integrated prediction models for other protein–peptide interactions.     

Stereochemical Structure–Activity Relationship of N-(2,3-Epoxypropyl)-N-(α-methylbenzyl)benzenesulfonamide Derivatives

The absolute configurations of two asymmetric centers in four stereoisomers of N-(2,3-epoxypropyl)-N-(α-methylbenzyl)benzenesulfonamide were determined and their biological activities were tested. Consequently, N-[(R)-2,3-epoxypropyl]-N-[(R)-α-methylbenzyl]benzenesulfonamide was found to be the most active isomer and the stereochemistry of the benzyl position was found to be more important than that of C₂ in the epoxypropyl group for biological activity.     

FFA1 (GPR40) Receptor Agonists Based on Phenylpropanoic Acid as Hypoglycemic Agents: Structure–Activity Relationship

Russian Journal of Bioorganic Chemistry - Free fatty acid receptor-1 (FFA1) agonists have been considered for a long time as a potentially new class for the treatment of type 2 diabetes mellitus....     

Studies on Chemical Structure Modification and Structure?Activity Relationship of Derivatives of Gambogic Acid at C(39)

The natural product gambogic acid exhibits high potency in inhibiting cancer cell lines. Rational medicinal modifications on gambogic acid will improve its physicochemical properties and drug‐like characters. To investigate the structure? activity relationship of gambogic acid and also to find rational modification position on its chemical skeleton, we designed, synthesized, and characterized 16 derivatives of gambogic acid that were modified at C(39). The structure? activity relationships (SARs) were discussed. The anti‐proliferation data were accquired through MTT (=3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl‐2H‐tetrazolium bromide) assays of A549, BGC823, U251, HepG2, and MDA‐MB‐231 cancer cell lines. Most of the synthesized compounds showed strong inhibitory effects. The SAR study revealed that derivatives with aliphatic amino moieties at C(39) were more potent than those with other substituents. The C(39) position can undergo different kinds of chemical modifications without leading to loss of activity. Compounds 4 and 6 can serve as potential lead compounds for further development of new anticancer drugs.     

A Synthetic Peptide Derived from NK-Lysin with Activity Against <Emphasis Type=Italic>Mycobacterium tuberculosis</Emphasis> and its Structure–Function Relationship

As appearance of drug resistant and multidrug resistant strains of Mycobacterium tuberculosis, antibiotics were no longer the only way to inhibit M. tuberculosis. It was shown that the porcine peptide NK-lysin is active against various microbes by interacting with microbial membranes. The NK-lysin-derived peptide has been demonstrated to possess stronger effect. Under this motivation, we synthesized a short peptide (N22) derived from an active fragment of NK-lysin—an important antimycobaterial domain involving the loop and the α-helical structure. Furthermore, we studied its stability and biological activity in vitro. The results showed that it inhibited the growth of M. tuberculosis H37Rv and had a low toxicity to human erythrocyte.     

Function and Structure Studies of GH Family 31 and 97 α-Glycosidases

A huge number of glycoside hydrolases are classified into the glycoside hydrolase family (GH family) based on their amino-acid sequence similarity. The glycoside hydrolases acting on α-glucosidic linkage are in GH family 4, 13, 15, 31, 63, 97, and 122. This review deals mainly with findings on GH family 31 and 97 enzymes. Research on two GH family 31 enzymes is described: clarification of the substrate recognition of Escherichia coli α-xylosidase, and glycosynthase derived from Schizosaccharomyces pombe α-glucosidase. GH family 97 is an aberrant GH family, containing inverting and retaining glycoside hydrolases. The inverting enzyme in GH family 97 displays significant similarity to retaining α-glycosidases, including GH family 97 retaining α-glycosidase, but the inverting enzyme has no catalytic nucleophile residue. It appears that a catalytic nucleophile has been eliminated during the molecular evolution in the same way as a man-made nucleophile mutant enzyme, which catalyzes the inverting reaction, as in glycosynthase and chemical rescue.     

Studies on Chemical‐Structure Modification and Structure?Activity Relationship of Gambogic Acid Derivatives at Carbon(34)

Gambogic acid (GA), a natural product, was identified as a promising antitumor agent. To further explore the structure? activity relationship of GA and discover novel GA derivatives as antitumor agents, 19 novel GA derivatives modified at C(34) were synthesized and evaluated against A549, BGC‐823, U251, HepG2, and MB‐231 cancer cell lines by cellular assays. Among them, 15 compounds were found to be more potent than GA against some cancer cell lines. Notably, compound 3 possessed potent inhibitory activities against five cell lines with IC₅₀ values ranging between 0.24 and 1.09 μM . Compounds 9 and 18 were seven to eightfold more active than GA against A549 cell line. Chemical modification at C(34) of GA by introducing of hydrophilic aliphatic amines resulted in increased activity and improved drug‐like properties. These findings will enhance our understanding of the SAR of GA and can lead to the discovery of novel GA derivatives as potential antitumor agents.     

Structure–Function Relationships of the Vasopressin Prohormone Domains

1. In this review the structure–function relationships of the different vasopressin prohormone domains are dated and discussed, with special reference to the neurophysin and glycopeptide domains.2. The primary structures of the currently known neurophysins and glycopeptide sequences are compared and discussed.3. The hormone-binding and aggregational properties of neurophysin are reviewed and related to a possible function within the regulated secretory pathway.4. It is proposed, based on the properties reviewed here as well as our own data shown here, that the sorting of the vasopressin prohormone is initiated by hormone binding, which triggers aggregation of the prohormone into the characteristic dense cores of the regulated secretory pathway.5. This may suggest that prohormone sorting into the regulated secretory pathway is, in general, determined by noncovalent, intramolecular interactions that promote aggregation.     

Structure–Function Analysis of the ADAM Family of Disintegrin-Like and Metalloproteinase-Containing Proteins (Review)

The ADAMs belong to a disintegrin-like and metalloproteinase-containing protein family that are zinc-dependent metalloproteinases. These proteins share all or some of the following domain structure: a signal peptide, a propeptide, a metalloproteinase, a disintegrin, a cysteine-rich, and an epidermal growth factor (EGF)-like domains, a transmembrane region, and a cytoplasmic tail. ADAMs are widely distributed in many organs, tissues, and cells, such as brain, testis, epididymis, ovary, breast, placenta, liver, heart, lung, bone, and muscle. These proteins are capable of four potential functions: proteolysis, adhesion, fusion, and intracellular signaling. Because the number of ADAM genes has grown rapidly and the biological functions of most members are unclear, this review analyzes the protein structures and functions, their activation and processing, their known and potential activities, and their evolutionary relationships. A sequence alignment of human ADAMs is compiled and their homology and physical data are calculated. The conceivable functions of ADAMs in reproduction, development, and diseases are also discussed.     

Studies on Taka-α-amylase (8)

This paper deals with some properties of reversibly inact. TAA effected by means of EDTA. The mechanism of EDTA inactivation was discussed from the view point that EDTA has a conspicious suppressive effect on the reactivation of heat-inact. enzyme, while it has no effect on the active enzyme itself. Particular attention was paid to the problem of calcium transfer along with the progress of inactivation.     

Novel Structure–Function Information on Biogenic Amine Transporters Revealed by Site-Directed Mutagenesis and Alkylation

The study reported by Wenge and Bönisch in this issue provides critical structural information regarding extracellular loop 2 (EL2) of the human norepinephrine transporter (NET). A systematic search among all 10 cysteine and 13 histidine residues in NET led to His222 in EL2 as the target for N-ethylmaleimide: its alkylation interferes with [³H]nisoxetine binding, indicating the part of EL2 containing His 222 reaches back into the protein interior where it prevents access by nisoxetine to its binding site. Thus, EL2 in human NET does much more than conformationally assisting substrate translocation. The present study underscores the importance of site-directed mutagenesis approaches to elucidate structural features that cannot be deduced from crystals of homolog proteins. In the case of NET, the closest crystal structure is that of the homolog LeuT, but EL2 is difficult to align with 22 less loop residues in LeuT than in NET. The present results could only be achieved by the systematic mutagenesis study of all cysteines and all histidines in NET.     

The Effects of Lanthanoid on the Structure–Function of Lactate Dehydrogenase from Mice Heart

The activity of lactate dehydrogenase (LDH, EC1.1.1.27) is often changed upon inflammatory responses in animals. Lanthanoid (Ln) was shown to provoke various inflammatory responses both in rats and mice; however, the molecular mechanism by which Ln³⁺ exert its toxicity has not been completely understood, especially that we know little about the mechanism of the interaction between Ln with 4f electron shell and alternation valence and LDH. In this report, we investigated the mechanisms of LaCl₃, CeCl₃, and NdCl₃ on LDH activity in vivo and in vitro. Our results showed that La³⁺, Ce³⁺, and Nd³⁺ could significantly activate LDH in vivo and in vitro; the order of activation was Ce³⁺?>?Nd³⁺?>?La³⁺?>?control. The affinity of LDH for Ce³⁺ was higher than Nd³⁺ and La³⁺; the saturated binding sites for Ce³⁺ on the LDH protein were 1.2 and for La³⁺ and Nd³⁺ 1.55. Ln³⁺ caused the reduction of exposure degree of cysteine or tryptophan/tyrosine of LDH, the increase of space resistance, and the enhancement of α-helix in secondary structure of LDH, which was greatest in Ce³⁺ treatment, medium in Nd³⁺ treatment, and least in La³⁺ treatment. It implied that the changes of structure–function on LDH caused by Ln³⁺ were closely related to the characteristics of 4f electron shell and alternation valence in Ln.     

Structure–Activity Relationship of novel phenylacetic CXCR1 inhibitors

We reported recently the Structure–Activity Relationship (SAR) of a class of CXCL8 allosteric modulators. They invariably share a 2-arylpropionic moiety so far considered a key structural determinant of the biological activity. We show the results of recent SAR studies on a novel series of phenylacetic derivatives supported by a combined approach of mutagenesis experiments and conformational analysis. The results suggest novel insights on the fine role of the propionic/acetic chain in the modulation of CXCL8 receptors.     

Structure-Activity Relationship of Synthetic Variants of the Milk-Derived Antimicrobial Peptide αs2-Casein f(183–207)

Template-based studies on antimicrobial peptide (AMP) derivatives obtained through manipulation of the amino acid sequence are helpful to identify properties or residues that are important for biological activity. The present study sheds light on the importance of specific amino acids of the milk-derived α_s2-casein f(183–207) peptide to its antibacterial activity against the food-borne pathogens Listeria monocytogenes and Cronobacter sakazakii. Trimming of the peptide revealed that residues at the C-terminal end of the peptide are important for activity. Removal of the last 5 amino acids at the C-terminal end and replacement of the Arg at position 23 of the peptide sequence by an Ala residue significantly decreased activity. These findings suggest that Arg23 is very important for optimal activity of the peptide. Substitution of the also positively charged Lys residues at positions 15 and 17 of the α_s2-casein f(183–207) peptide also caused a significant reduction of the effectiveness against C. sakazakii, which points toward the importance of the positive charge of the peptide for its biological activity. Indeed, simultaneous replacement of various positively charged amino acids was linked to a loss of bactericidal activity. On the other hand, replacement of Pro residues at positions 14 and 20 resulted in a significantly increased antibacterial potency, and hydrophobic end tagging of α_s2-casein f(193–203) and α_s2-casein f(197–207) peptides with multiple Trp or Phe residues significantly increased their potency against L. monocytogenes. Finally, the effect of pH (4.5 to 7.4), temperature (4°C to 37°C), and addition of sodium and calcium salts (1% to 3%) on the activity of the 15-amino-acid α_s2-casein f(193–207) peptide was also determined, and its biological activity was shown to be completely abolished in high-saline environments.     

Studies on 5′-Phosphodiesterases in Microorganisms

5′-Phosphodiesterase, which degrades RNA into nucleoside-5′-monophosphates but does not attack DNA, is present not only in mycelium but also in culture filtrate of Penicillium citrinum Thorn 1131. For the formation of this enzyme pH of the culture medium must be kept below 7.0 during culture, as this enzyme is inactivated rapidly in alkaline solution. The pH optimum of this enzyme is in the region of pH 5. Cysteine, Mg⁺⁺, sodium fluoride, and inorganic ortho- or pyrophosphate are without appreciable effect on this enzyme. Nucleoside-5′-monophosphates, which have been regarded as new chemical seasonings, can be produced economically in a large scale by using the microbial 5′-phosphodiesterase.