Translation of structure‐activity relationships from cyclic mixed efficacy opioid peptides to linear analogues

Most opioid analgesics used in the treatment of pain are mu opioid receptor (MOR) agonists. While effective, there are significant drawbacks to opioid use, including the development of tolerance and dependence. However, the coadministration of a MOR agonist with a delta opioid receptor (DOR) antagonist slows the development of MOR‐related side effects, while maintaining analgesia. We have previously reported a series of cyclic mixed efficacy MOR agonist/DOR antagonist ligands. Here we describe the transfer of key features from these cyclic analogs to linear sequences. Using the linear MOR/DOR agonist, Tyr‐DThr‐Gly‐Phe‐Leu‐Ser‐NH 2 ( DTLES ), as a lead scaffold, we replaced Phe 4 with bulkier and/or constrained aromatic residues shown to confer DOR antagonism in our cyclic ligands. These replacements failed to confer DOR antagonism in the DTLES analogs, presumably because the more flexible linear ligands can adopt binding poses that will fit in the narrow binding pocket of the active conformations of both MOR and DOR. Nonetheless, the pharmacological profile observed in this series, high affinity and efficacy for MOR and DOR with selectivity relative to KOR, has also been shown to reduce the development of unwanted side effects. We further modified our lead MOR/DOR agonist with a C‐terminal glucoserine to improve bioavailability. The resulting ligand displayed high efficacy and potency at both MOR and DOR and no efficacy at KOR. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 107–114, 2014.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102641/1/bip22437.pd

The role of hydrophobic interactions in positioning of peripheral proteins in membranes

Abstract Background Three-dimensional (3D) structures of numerous peripheral membrane proteins have been determined. Biological activity, stability, and conformations of these proteins depend on their spatial positions with respect to the lipid bilayer. However, these positions are usually undetermined. Results We report the first large-scale computational study of monotopic/peripheral proteins with known 3D structures. The optimal translational and rotational positions of 476 proteins are determined by minimizing energy of protein transfer from water to the lipid bilayer, which is approximated by a hydrocarbon slab with a decadiene-like polarity and interfacial regions characterized by water-permeation profiles. Predicted membrane-binding sites, protein tilt angles and membrane penetration depths are consistent with spin-labeling, chemical modification, fluorescence, NMR, mutagenesis, and other experimental studies of 53 peripheral proteins and peptides. Experimental membrane binding affinities of peripheral proteins were reproduced in cases that did not involve a helix-coil transition, specific binding of lipids, or a predominantly electrostatic association. Coordinates of all examined peripheral proteins and peptides with the calculated hydrophobic membrane boundaries, subcellular localization, topology, structural classification, and experimental references are available through the Orientations of Proteins in Membranes (OPM) database. Conclusion Positions of diverse peripheral proteins and peptides in the lipid bilayer can be accurately predicted using their 3D structures that represent a proper membrane-bound conformation and oligomeric state, and have membrane binding elements present. The success of the implicit solvation model suggests that hydrophobic interactions are usually sufficient to determine the spatial position of a protein in the membrane, even when electrostatic interactions or specific binding of lipids are substantial. Our results demonstrate that most peripheral proteins not only interact with the membrane surface, but penetrate through the interfacial region and reach the hydrocarbon interior, which is consistent with published experimental studies.http://deepblue.lib.umich.edu/bitstream/2027.42/116604/1/12900_2007_Article_125.pd

Nutritional habits of combat athletes

The review presents modern data characterizing the features of the energy exchange of athletes engaged in combat sport. The general principles of diet formation for combat athletes taking into account the basis of optimal nutrition, dependence on the period of sports activity (training, competition, and recovery), the duration and intensity of physical exertion are described. Based on results of recent studies published by Russian and foreign authors, the substantiation for the energy density of chemical composition of the diet (the content of proteins, fats, carbohydrates, vitamins, macro- and microelement) and hydration regime of combat athletes is given. The issues of food distribution during the day are affected, depending on the training and competitive process. Particular attention is paid to the use of specialized products and dietary supplements, as well as personalization of nutrition, which is based on individual studying of the nutritional status of combat athletes

Evaluation of the actual nutrition and nutritional status of combat athletes

Objective: to evaluate the actual nutrition and nutritional status of combat athletes. Materials and methods: the evaluation of the actual nutrition of 129 athletes involved in martial arts: 86 men (average age 22.1±0.5 years) and 43 women (average age 22.2±0.8 years) were carried out. The actual nutrition was investigated by the method of 24-hour (daily) reproduction of food intake. The biochemical and anthropometric markers of the nutritional status were evaluated; body mass index (BMI) and component body composition were assessed using bioimpedansometry. Results: results of the study showed unbalanced nutrition of athletes - excessive consumption of animal fat, cholesterol, sodium, and added sugar (including high-fat dairy products and confectionery).The nutrition analysis of combat athletes revealed a lack of vitamins B, magnesium, calcium, which was associated with low consumption of dairy products, fruits and vegetables. Disturbances in the nutritional structure caused unfavorable changes in some participants, such as an increase in BMI, the amount of adipose tissue, dyslipidemia, against the background of insufficient efficiency of the recovery processes of athletes and the risk of overwork. Conclusions: violation of the nutritional structure of athletes leads to development of pathological changes in nutritional status, which include increase of BMI and the amount of adipose tissue, dyslipidemia due to the lack of efficiency of recovery processes of athletes and the risk of overwork. The noted violations of nutrition and nutritional status are a risk factor for the development of alimentary-dependent diseases (cardiovascular pathology, obesity, osteoporosis, etc.)

Study of the association of gene polymorphism with the risk of non-communicable diseases in martial artists

Objective: to study the effect of genetic polymorphisms: rs rs9939609 (FTO gene), rs4994 (ADRB3 gene), rs1042713 (ADRB2 gene), rs2228570 (VDR gene), rs1801133 (MTHFR gene) on anthropometric and lipid metabolism indicators in athletes representing martial arts.Materials and methods: studies of anthropometric and biochemical parameters, genetic polymorphisms were carried out in 120 athletes (101 men and 19 women) who are engaged in martial arts. Anthropometric studies were performed by measuring height (cm), body weight (kg), followed by calculating body mass index (BMI, kg / m2). Biochemical nutritional status markers were determined using the ABX Pentra 400 analyzer (HORIBA ABX SAS, France) in an automatic mode. Genotyping was performed using allele­specific amplification using TaqMan probes complementary to polymorphic DNA regions and real­time detection of the results using reagent kits from Syntol, Russia. Studies were performed on the device CFX96 Real Time System (Bio­Rad, USA). Statistical processing of the results was performed using the PASW Statistics 20 system.Results: as a result of generic Diovan athletes martial artists on the risk of non­communicable diseases, discovered that the frequency of allele A of rs9939609 polymorphism of the FTO gene they have is 43.9 %, allele polymorphism rs4994 ADRB3 gene — 10.9 %, G allele of rs1042713 ADRB2 gene polymorphism — 52.6 %, G allele of the polymorphism rs2228570 VDR gene with 44.9 % and allele t of rs1801133 in the MTHFR gene to 36.7 %. An association was found between the value of anthropometric indicators in male martial artists and the presence of polymorphisms rs9939609 (FTO), rs1042713 (ADRB2) and rs2228570 (VDR).Conclusions: the reason for the identified dyslipidemia in martial artists may be not only the previously detected violations of the structure of their nutrition, but also the presence of certain genetic polymorphisms, in particular, rs4994 of the ADRB3 gene and rs1042713 of the ADRB2 gene

Study of Association of gene polymorphism with nutrition and nutritional status of martial arts athletes

Objective: studying the effect of genetic polymorphisms: rs1815739 (ACTN3 gene), rs2016520 (PPARD gene), rs1042713 (ADRB2 gene), rs1799945 (HFE gene) on anthropometric and lipid metabolism indicators in athletes representing martial arts. Materials and methods: studies of anthropometric and biochemical parameters, genetic polymorphisms were carried out in 83 athletes (64 men and 19 women) who were are engaged in martial arts. Anthropometric studies were performed by height (cm) and body weight (kg) measuring followed by calculating body mass index (BMI, kg / m2). Biochemical nutritional status markers were determined using the ABXPENTRA 400 analyzer (HORIBA ABX SAS, France) in an automatic mode. Genotyping was performed using allele-specific amplification using TaqMan probes complementary to polymorphic DNA regions and realtime detection of the results using reagent kits from Syntol, Russia. Studies were performed on the device «CFX96 Real Time System» («BIO-RAD», USA). Statistical processing of the results was performed using the PASW Statistics 20 system. Results: as a result of gene testing for endurance of combat athletes, it was found that the frequency of the T allele of the rs1815739 polymorphism (ACTN3 gene) was 47.5%, the PPARD gene ал20120120 allele G is 13.9%, the rs1042713 G allele of the ADRB2 gene was 51.9%, and the G allele of the rs1799945 polymorphism of the HFE gene was 19.3%. No association was found between the value of anthropometric parameters in athletes and the presence of the studied polymorphisms. Conclusions: the cause of identified dyslipidemia in combat athletes may be not only the disturbances in the structure of their nutrition that we found earlier, but also the presence of certain genetic polymorphisms

Structural organization of G-protein-coupled receptors

Atomic-resolution structures of the transmembrane 7-α-helical domains of 26 G-protein-coupled receptors (GPCRs) (including opsins, cationic amine, melatonin, purine, chemokine, opioid, and glycoprotein hormone receptors and two related proteins, retinochrome and Duffy erythrocyte antigen) were calculated by distance geometry using interhelical hydrogen bonds formed by various proteins from the family and collectively applied as distance constraints, as described previously [Pogozheva et al., Biophys. J., 70 (1997) 1963]. The main structural features of the calculated GPCR models are described and illustrated by examples. Some of the features reflect physical interactions that are responsible for the structural stability of the transmembrane α-bundle: the formation of extensive networks of interhelical H-bonds and sulfur–aromatic clusters that are spatially organized as 'polarity gradients' the close packing of side-chains throughout the transmembrane domain; and the formation of interhelical disulfide bonds in some receptors and a plausible Zn2+ binding center in retinochrome. Other features of the models are related to biological function and evolution of GPCRs: the formation of a common 'minicore' of 43 evolutionarily conserved residues; a multitude of correlated replacements throughout the transmembrane domain; an Na+-binding site in some receptors, and excellent complementarity of receptor binding pockets to many structurally dissimilar, conformationally constrained ligands, such as retinal, cyclic opioid peptides, and cationic amine ligands. The calculated models are in good agreement with numerous experimental data.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42965/1/10822_2004_Article_200887.pd

Life at the border: Adaptation of proteins to anisotropic membrane environment

This review discusses main features of transmembrane (TM) proteins which distinguish them from water‐soluble proteins and allow their adaptation to the anisotropic membrane environment. We overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co‐translational and post‐translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large‐scale conformational transitions during membrane insertion and transport function. Special attention is paid to the polarity of TM protein surfaces described by profiles of dipolarity/polarizability and hydrogen‐bonding capacity parameters that match polarity of the lipid environment. Analysis of distributions of Trp resides on surfaces of TM proteins from different biological membranes indicates that interfacial membrane regions with preferential accumulation of Trp indole rings correspond to the outer part of the lipid acyl chain region—between double bonds and carbonyl groups of lipids. These “midpolar” regions are not always symmetric in proteins from natural membranes. We also examined the hydrophobic effect that drives insertion of proteins into lipid bilayer and different free energy contributions to TM protein stability, including attractive van der Waals forces and hydrogen bonds, side‐chain conformational entropy, the hydrophobic mismatch, membrane deformations, and specific protein–lipid binding.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108308/1/pro2508.pd

Design of high affinity cyclic pentapeptide ligands for Κ-opioid receptors

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73319/1/j.1399-3011.2005.00295.x.pd

Pharmacophore and receptor models for neurokinin receptors

Three neurokinin (NK) antagonist pharmacophore models (Models 1–3) accounting for hydrogen bonding groups in the `head' and `tail' of NK receptor ligands have been developed by use of a new procedure for treatment of hydrogen bonds during superimposition. Instead of modelling the hydrogen bond acceptor vector in the strict direction of the lone pair, an angle is allowed between the hydrogen bond acceptor direction and the ideal lone pair direction. This approach adds flexibility to hydrogen bond directions and produces more realistic RMS values. By using this approach, two novel pharmacophore models were derived (Models 2 and 3) and a hydrogen bond acceptor was added to a previously published NK2 pharmacophore model [Poulsen et al., J. Comput.-Aided Mol. Design, 16 (2002) 273] (Model 1). Model 2 as well as Model 3 are described by seven pharmacophore elements: three hydrophobic groups, three hydrogen bond acceptors and a hydrogen bond donor. Model 1 contains the same hydrophobic groups and hydrogen bond donor as Models 2 and 3, but only one hydrogen bond acceptor. The hydrogen bond acceptors and donor are represented as vectors. Two of the hydrophobic groups are always aromatic rings whereas the other hydrophobic group can be either aromatic or aliphatic. In Model 1 the antagonists bind in an extended conformation with two aromatic rings in a parallel displaced and tilted conformation. Model 2 has the same two aromatic rings in a parallel displaced conformation whereas Model 3 has the rings in an edge to face conformation. The pharmacophore models were evaluated using both a structure (NK receptor homology models) and a ligand based approach. By use of exhaustive conformational analysis (MMFFs force field and the GB/SA hydration model) and least-squares molecular superimposition studies, 21 non-peptide antagonists from several structurally diverse classes were fitted to the pharmacophore models. More antagonists could be fitted to Model 2 with a low RMS and a low conformational energy penalty than to Models 1 and 3. Pharmacophore Model 2 was also able to explain the NK1, NK2 and NK3 subtype selectivity of the compounds fitted to the model. Three NK 7TM receptor models were constructed, one for each receptor subtype. The location of the antagonist binding site in the three NK receptor models is identical. Compounds fitted to pharmacophore Model 2 could be docked into the NK1, NK2 and NK3 receptor models after adjustment of the conformation of the flexible linker connecting the head and tail. Models 1 and 3 are not compatible with the receptor models.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42969/1/10822_2004_Article_5257316.pd