Combinatorial peptide library screening for discovery of diverse α-glucosidase inhibitors using molecular dynamics simulations and binary QSAR models

Human α-glucosidase is an enzyme involved in the catalytic cleavage of the glucoside bond and involved in numerous functionalities of the organism, as well as in the insurgence of diabetes mellitus 2 and obesity. Thus, developing chemicals that inhibit this enzyme is a promising approach for the treatment of several pathologies. Small peptides such as di- and tri-peptides may be in natural organism as well as in the GI tract in high concentration, coming from the digestive process of meat, wheat and milk proteins. In this work, we reported the first tentative hierarchical structure-based virtual screening of peptides for human α-glucosidase. The goal of this work is to discover novel and diverse lead compounds that my act as inhibitors of α-glucosidase such as small peptides by performing a computer aided virtual screening and to find novel scaffolds for further development. Thus, in order to select novel candidates with original structure we performed molecular dynamics (MD) simulations among the 12 top-ranked peptides taking as comparison the MD simulations performed on crystallographic inhibitor acarbose. The compounds with the lower RMSD variability during the MD, were reserved for in vitro biological assay. The selected 4 promising structures were prepared on solid phase peptide synthesis and used for the inhibitory assay, among them compound 2 showed good inhibitory activity, which validated our method as an original strategy to discover novel peptide inhibitors. Moreover, pharmacokinetic profile predictions of these 4 peptides were also carried out with binary QSAR models using MetaCore/MetaDrug applications.     

Long-term follow-up of total penile reconstruction with sensate osteocutaneous free fibula flap in 18 biological male patients

Surgical reconstruction of the penis is challenging because of the many cosmetic and functional (e.g., sexual intercourse and voiding) requirements that must be addressed. Since the free sensate osteocutaneous fibula flap was first described for total penile reconstruction in 1993 it has been widely accepted, with its advantages and minimal shortcomings. In this article, the authors present the longest follow-up of biologically male patients with free fibular phalloplasties. Since 1994, 18 biologically male patients with total penile losses for various reasons were treated with free sensate osteocutaneous fibula flaps. All patients were included in the study. The ages of the patients ranged between 20 and 26 years (mean, 22.2 years). The average follow-up period was 5.4 years (range, 1 to 9 years). Patient satisfaction was evaluated by a questionnaire regarding both quality of orgasm and daily activities. Conventional radiographic imaging, magnetic resonance imaging, and bone mineral densitometry were performed to evaluate the fate of the bony component of the flap. Also, sensibility was evaluated by bulbocavernous reflex and penile somatosensory evoked potentials testing in nine patients. Six patients married, and five of them had six children. Most patients and their partners reported pleasurable sexual intercourse and orgasm. Conventional radiographs of the fibular bone in neophalluses showed robust, calcified bone structure without any evidence of bone resorption or fracture. The magnetic resonance images showed the cortical substance and spongiosum of the bone marrow, which are characteristic signs of bone viability. After intravenous injection of gadolinium, the neophallus bone showed uptake of contrast medium. Viability of neophallus bone was shown even at 9-year follow-up (the longest follow-up in the literature). Dual energy x-ray absorptiometry measurements of the penile bone grafts showed that fibular components in the penis had bone mineral density values that were close to but lower than those of intact fibula in the same subjects. These results were considered as evidence of viability of bone grafts. Neural integrity was found between the nerves of the neophallus and the residual penile bodies by both bulbocavernous reflex and penile somatosensory evoked potentials tests. In conclusion, free sensate fibula flap phalloplasty provides the cosmetic and functional requirements that an ideal penis should have. All results put an end to the discussion that the fibular component of the neophallus could resorb. Constitution of neural integrity is important in terms of pleasurable sexual intercourse. The authors believe the free sensate osteocutaneous fibula flap should be considered as the standard in penile reconstruction.     

Synthesis and biological evaluation of novel curcumin analogs as anti-cancer and anti-angiogenesis agents

A series of novel curcumin analogs were synthesized and screened for anti-cancer and anti-angiogenesis activities at Emory University and at the National Cancer Institute (NCI). These compounds are symmetrical alpha,beta-unsaturated and saturated ketones. The majority of the analogs demonstrated a moderate degree of anti-cancer activity. Compounds 10, 11, and 14 exhibited a high degree of cytotoxicity in the NCI in vitro anti-cancer cell line screen. In addition, this screen revealed that these compounds inhibit tumor cell growth with a higher potency than the commonly used chemotherapeutic drug, cisplatin. In independent in vitro screens conducted at Emory, the same compounds plus 4, 5, 8, 9, and 13 exhibited a high degree of cytotoxicity to tumor cells. Analogs that were effective in the anti-cancer screens were also effective in in vitro anti-angiogenesis assays. Compounds 4, 9, 11, and 14 were most effective in the anti-angiogenesis assays run at Emory. In the assays conducted by the NCI, compound 14 was almost as potent as the anti-angiogenic drug TNP-470, which has undergone clinical trials. Based on the favorable in vitro anti-cancer and anti-angiogenesis results with 14, further in vivo tests were conducted. This compound effectively reduced the size of human breast tumors grown in female athymic nude mice and showed little toxicity. This data, coupled with the remarkable in vitro data, suggests that compound 14 may potentially be an effective chemotherapeutic agent. As a follow-up, a 3D quantitative structure relationship based on 14 has been developed. It shows a cross-validated r2(q2) and a predictive r2(p2) = 0.71. COMPARE analysis suggests the compound to be a possible RNA/DNA antimetabolite, but also implies that the compound's cytotoxicity may arise from a presently unknown mechanism.     

Gramicidin A channel as a test ground for molecular dynamics force fields

We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K(+) ion is calculated along the channel axis using the umbrella sampling method. Calculations are performed using two of the most common force fields in MD simulations: CHARMM and GROMACS. Both force fields lead to large central barriers for K(+) ion permeation, that are substantially higher than those deduced from the physiological data by inverse methods. In long MD simulations lasting over 60 ns, several ions are observed to enter the binding site but none of them crossed the channel despite the presence of a large driving field. The present results, taken together with many earlier studies, highlights the shortcomings of the standard force fields used in MD simulations of ion channels and calls for construction of more appropriate force fields for this purpose.     

Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels

We demonstrated previously that the two continuum theories widely used in modeling biological ion channels give unreliable results when the radius of the conduit is less than two Debye lengths. The reason for this failure is the neglect of surface charges on the protein wall induced by permeating ions. Here we attempt to improve the accuracy of the Poisson-Boltzmann and Poisson-Nernst-Planck theories, when applied to channel-like environments, by including a specific dielectric self-energy term to overcome spurious shielding effects inherent in these theories. By comparing results with Brownian dynamics simulations, we show that the inclusion of an additional term in the equations yields significant qualitative improvements. The modified theories perform well in very wide and very narrow channels, but are less successful at intermediate sizes. The situation is worse in multi-ion channels because of the inability of the continuum theories to handle the ion-to-ion interactions correctly. Thus, further work is required if these continuum theories are to be reliably salvaged for quantitative studies of biological ion channels in all situations.     

Modeling diverse range of potassium channels with Brownian dynamics

Using the experimentally determined KcsA structure as a template, we propose a plausible explanation for the diversity of potassium channels seen in nature. A simplified model of KcsA is constructed from its atomic resolution structure by smoothing out the protein-water boundary and representing the atoms forming the channel protein as a homogeneous, low dielectric medium. The properties of the simplified and atomic-detail models, deduced from electrostatic calculations and Brownian dynamics simulations, are shown to be qualitatively similar. We then study how the current flowing across the simplified model channel changes as the shape of the intrapore region is modified. This is achieved by increasing the radius of the intracellular pore systematically from 1.5 to 5 A while leaving the dimensions of the selectivity filter and inner chamber unaltered. The strengths of the dipoles located near the entrances of the channel, the carbonyl groups lining the selectivity filter, and the helix macrodipoles are kept constant. The channel conductance increases steadily as the radius of the intracellular pore is increased. The rate-limiting step for both the outward and inward current is the time it takes for an ion to cross the residual energy barrier located in the intrapore region. The current-voltage relationship obtained with symmetrical solutions is linear when the applied potential is less than approximately 100 mV but deviates slightly from Ohm's law at higher applied potentials. The nonlinearity in the current-voltage curve becomes less pronounced as the radius of the intracellular pore is increased. When the strengths of the dipoles near the intracellular entrance are reduced, the channel shows a pronounced inward rectification. Finally, the conductance exhibits the saturation property observed experimentally. We discuss the implications of these findings on the transport of ions across the potassium channels and membrane channels in general.     

Comparison of circadian rhythm characteristics of blood pressure and heart rate in patients before and after elective coronary artery bypass surgery

Coronary artery bypass grafting surgery (CABGS) is done to reperfuse the ischemic myocardium of coronary disease patients. This study was designed to analyze the circadian rhythm characteristics of blood pressure (BP) and heart rate (HR) of patients before and after CABGS. Fifty-one patients undergoing elective CABGS were studied; 21 patients received one, 12 two and 18 three or more grafts. BP was monitored for 24h before and after CABGS while patients were recumbent in the hospital. Systolic (S) and diastolic (D) BP and HR were assessed every 30 min. Of the 51 patients, 37 (73%) had nondipper 24h BP patterns (nocturnal decline in BP < 10% of daytime mean level) in the preoperative baseline assessment. The peak and MESOR (rhythm-adjusted 24h mean) values of the circadian rhythm in SBP, DBP, and pulse pressure (PP) significantly declined following surgery, while HR and rate-pressure product (RPP = SBP x HR) markedly increased. The double amplitude (peak-to-trough variation) of the circadian rhythm in SBP and DBP was significantly reduced postoperatively, and that of the rhythm in HR and RPP significantly increased. The slopes of the morning rise and evening dip in the 24h SBP profile were reduced significantly after bypass grafting. The corresponding slopes of the HR profile, in contrast, were markedly increased.     

G-CSF Predicts Cardiovascular Events in Patients with Stable Coronary Artery Disease

Granulocyte-colony-stimulating-factor (G-CSF) induces mobilization of progenitor cells but may also exert pro-inflammatory and pro-thrombotic effects. Treatment with recombinant G-CSF after acute myocardial infarction is currently under examination and has been associated with in-stent restenosis. However, it is not known whether plasma levels of endogenous G-CSF are also associated with an increased cardiovascular risk. Therefore we included 280 patients with angiographically proven stable coronary artery disease. G-CSF was measured by specific ELISA and patients were followed for a median of 30 months for the occurrence of major adverse cardiovascular events (MACE: death, myocardial infarction, re-hospitalization). Those with cardiac events during follow-up showed significant higher G-CSF levels (32.3 pg/mL IQR 21.4–40.5 pg/mL vs. 24.6 pg/mL IQR 16.4–34.9 pg/mL; p<0.05) at baseline. Patients with G-CSF plasma levels above the median had a 2-fold increased risk for MACE (p<0.05). This was independent from established cardiovascular risk factors. In addition, G-CSF above the median was a predictor of clinical in-stent restenosis after implantation of bare-metal stents (6.6% vs. 19.4%; p<0.05) but not of drug-eluting stents (7.7% vs. 7.6%; p = 0.98). This data suggests that endogenous plasma levels of G-CSF predict cardiovascular events independently from established cardiac risk factors and are associated with increased in-stent restenosis rates after implantation of bare metal stents.