Eric S. Manas

Water structure changes induced by hydrophobic and polar solutes revealed by simulations and infrared spectroscopy

A combination of simulations and Fourier transform infrared spectroscopy was used to examine the effect of three ionic solutes (KCl, NaCl, and KSCN), the polar solute urea, and the osmolyte trimethylamine-N-oxide (TMAO) on a water structure. The ionic solutes increase the mean water–water H-bond angle in their first hydration shell concomitantly shifting the OH stretching mode to higher frequency, and shifting the HOH bending mode to lower frequency. TMAO decreases the mean water–water H-bond angle in its first hydration shell, shifts the OH stretching mode frequency down, and shifting the HOH bending mode frequency up. Urea has no effect on the mean H-bond angle, OH stretch, and HOH bend frequencies. These results can be explained in terms of changes in the relative proportions of two H-bond angle populations: Ionic solutes increase the population of more distorted (larger angle) H bonds relative to the less distorted population, TMAO has the reverse effect, while urea does not affect the H-bond angle probability distribution. The negligible effect of urea on water structure supports the direct binding model for urea-induced protein denaturation.A combination of simulations and Fourier transform infrared spectroscopy was used to examine the effect of three ionic solutes (KCl, NaCl, and KSCN), the polar solute urea, and the osmolyte trimethylamine-N-oxide (TMAO) on a water structure. The ionic solutes increase the mean water–water H-bond angle in their first hydration shell concomitantly shifting the OH stretching mode to higher frequency, and shifting the HOH bending mode to lower frequency. TMAO decreases the mean water–water H-bond angle in its first hydration shell, shifts the OH stretching mode frequency down, and shifting the HOH bending mode frequency up. Urea has no effect on the mean H-bond angle, OH stretch, and HOH bend frequencies. These results can be explained in terms of changes in the relative proportions of two H-bond angle populations: Ionic solutes increase the population of more distorted (larger angle) H bonds relative to the less distorted population, TMAO has the reverse effect, while urea does not affect the H-bond angle pr...

Identification of novel estrogen receptor α antagonists

Abstract We have identified novel estrogen receptor alpha (ERα) antagonists using both cell-based and computer-based virtual screening strategies. A mammalian two-hybrid screen was used to select compounds that disrupt the interaction between the ERα ligand binding domain (LBD) and the coactivator SRC-3. A virtual screen was designed to select compounds that fit onto the LxxLL peptide-binding surface of the receptor, based on the X-ray crystal structure of the ERα LBD complexed with a LxxLL peptide. All selected compounds effectively inhibited 17-β-estradiol induced coactivator recruitment with potency ranging from nano-molar to micromolar. However, in contrast to classical ER antagonists, these novel inhibitors poorly displace estradiol in the ER-ligand competition assay. Nuclear magnetic resonance (NMR) suggested direct binding of these compounds to the receptors pre-complexed with estradiol and further demonstrated that no estradiol displacement occurred. Partial proteolytic enzyme digestion revealed that, when compared with 17-β-estradiol- and 4 hydroxy-tamoxifen (4-OHT) bound receptors, at least one of these compounds might induce a unique receptor conformation. These small molecules may represent new classes of ER antagonists, and may have the potential to provide an alternative for the current anti-estrogen therapy.

Discovery and initial optimization of 5,5'-disubstituted aminohydantoins as potent β-secretase (BACE1) inhibitors

8,8-Diphenyl-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine (1) was identified through HTS, as a weak (micromolar) inhibitor of BACE1. X-Ray crystallographic studies indicate the 2-aminoimidazole ring forms key H-bonding interactions with Asp32 and Asp228 in the catalytic site of BACE1. Lead optimization using structure-based focused libraries led to the identification of low nanomolar BACE1 inhibitors such as 20b with substituents which extend from the S(1) to the S(3) pocket.

Horseradish peroxidase monitored by infrared spectroscopy: effect of temperature, substrate and calcium

Horseradish peroxidase was examined as a function of Ca and substrate binding using infrared spectroscopy in the temperature range of 10-300 K. The Ca complex could be identified by the carboxylate stretches. The amide peak positions indicate that the protein remains stable from room temperature to 10 K. Shifts in these peaks are consistent with increased hydrogen bonding as temperature decreases, but the protein conformation is maintained at cryogenic temperatures. The substrate, benzohydroxamic acid, produced no detectable change in the infrared spectrum, consistent with X-ray crystallography results. With removal of Ca, the protein maintained its overall helicity.

Critical evaluation of methods to incorporate entropy loss upon binding in high‐throughput docking

Proper accounting of the positional/orientational/conformational entropy loss associated with protein–ligand binding is important to obtain reliable predictions of binding affinity. Herein, we critically examine two simplified statistical mechanics‐based approaches, namely a constant penalty per rotor method, and a more rigorous method, referred to here as the partition function‐based scoring (PFS) method, to account for such entropy losses in high‐throughput docking calculations. Our results on the estrogen receptor β and dihydrofolate reductase proteins demonstrate that, while the constant penalty method over‐penalizes molecules for their conformational flexibility, the PFS method behaves in a more “ΔG‐like” manner by penalizing different rotors differently depending on their residual entropy in the bound state. Furthermore, in contrast to no entropic penalty or the constant penalty approximation, the PFS method does not exhibit any bias towards either rigid or flexible molecules in the hit list. Preliminary enrichment studies using a lead‐like random molecular database suggest that an accurate representation of the “true” energy landscape of the protein–ligand complex is critical for reliable predictions of relative binding affinities by the PFS method. Proteins 2007.

Dual acting norepinephrine reuptake inhibitors and 5-HT2A receptor antagonists: Identification, synthesis and activity of novel 4-aminoethyl-3-(phenylsulfonyl)-1H-indoles

The discovery of a series of 4-aminoethyl-3-(phenylsulfonyl)-1H-indoles, dual acting norepinephrine reuptake inhibitors (NRIs) and 5-HT(2A) receptor antagonists, is described. The synthesis and structure-activity relationship (SAR) of this novel series of compounds is also presented.

Electronic interactions in metal complexed photoconducting polymers: a ZINDO study

Abstract Semi-empirical (INDO/s) calculations have been conducted on molecular fragments with zero to three phenylenevinylene (PV) units attached to 4 and 4 ′ positions of a 2,2 ′ -bipyridine (bpy) group, with and without chelated metal ions, mimicking metal-free and metal-chelated photoconducting polymers 1 and 2 [Chen et al., J. Phys. Chem. B 104 (2000) 1950]. The calculations suggest that: (1) a global lowering of the molecular orbital energy levels due to metal-chelation is responsible for the observed red-shift in the lowest energy transitions; and (2) metal chelation attenuates π -electron delocalization. The relevance of these effects to photoluminescence of metal-chelated polymers is also discussed.

Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening.

Elevated levels of human lipoprotein-associated phospholipase A2 (Lp-PLA2) are associated with cardiovascular disease and dementia. A fragment screen was conducted against Lp-PLA2 in order to identify novel inhibitors. Multiple fragment hits were observed in different regions of the active site, including some hits that bound in a pocket created by movement of a protein side chain (approximately 13 Å from the catalytic residue Ser273). Using structure guided design, we optimized a fragment that bound in this pocket to generate a novel low nanomolar chemotype, which did not interact with the catalytic residues.

Discovery of a new series of monoamine reuptake inhibitors, the 1-amino-3-(1H-indol-1-yl)-3-phenylpropan-2-ols.

A novel series of monoamine reuptake inhibitors, the 1-amino-3-(1H-indol-1-yl)-3-phenylpropan-2-ols, have been discovered by combining virtual and focused screening efforts with design techniques. Synthesis of the two diastereomeric isomers of the molecule followed by chiral resolution of each enantiomer revealed the (2R,3S)-isomer to be a potent norepinephrine reuptake inhibitor (IC(50)=28 nM) with excellent selectivity over the dopamine transporter and 13-fold selectivity over the serotonin transporter.