Pharmacoinformatics study of Piperolactam A from Piper betle root as new lead for non steroidal anti fertility drug development

Fertility control is a burning problem all over the world to regulate population overflow and maintain ecological balance. This study is an in-silico approach to explore a non-steroidal lead as contraceptive agent in order to avoid several contraindications generated by steroidal analogues. Piperolactam A, an aristolactam isolated from Piper betle Linn. showed binding affinity towards estrogen and progesterone receptor as −8.9 and −9.0 Kcal/mol (inhibition constant K_i = 0.294 μM and 0.249 μM) respectively which is even larger than that of reported antagonists such as Rohitukine and OrgC (binding affinity −8.7 and −8.4 Kcal/mol; K_i 0.443 μM and 0.685 μM respectively). The binding site exploration displayed more hydrogen bonding of Piperolactam A (His 524, Leu 346, Thr 347) than Rohitukine and OrgC (Leu 718) with associated receptors which was further confirmed by molecular dynamics simulations. The drug-likeliness of the compound has been proved from its tally with Lipinsky’s Rule of Five and lowered toxicity such as cardiac toxicity, liver toxicity, mutagenicity and ecological toxicity. Endocrine disruptome and later docking guided molecular simulations revealed that Piperolactam A has weaker binding affinity and/or lower probability of binding with nuclear receptors especially hERG and cytochrome P450. The high Caco-2 permeability suggested more bioavailability hence more therapeutic efficacy of the drug.     

The binding mode of picrotoxinin in GABAA-ρ receptors: Insight into the subunit’s selectivity in the transmembrane domain

The channel blocker picrotoxinin has been studied with GABA_A-ρ1 and GABA_A-ρ2 homology models based on the GluCl crystal structure. Picrotoxinin is tenfold more potent for GABA_A-ρ2 than for GABA_A-ρ1 homomeric channels. This intra-subunit selectivity arises from the unconserved residues at the 2’ sites, which are the essential molecular basis for both the binding and potency of picrotoxinin. The serine residues at the 2’ positions of the ρ2 channel are predicted to form multiple hydrogen bonds and hydrophobic interactions with picrotoxinin, whereas the proline residues in the 2’ positions of ρ1 channels are predicted to form only hydrophobic contacts with picrotoxinin. However, although the studied ρ1 P2’G, A, and V models form no hydrogen bonds with picrotoxinin, they may participate in several hydrophobic interactions, and the ligand may have distinctive binding modes with GABA_A-ρ mutant channels. Picrotoxinin has a lower Emodel value with ρ2 than ρ1 homomeric models (−47 Kcal/mol and −36 Kcal/mol, respectively), suggesting that picrotoxin blocks the pores of the ρ2 channels more effectively.     

Inhibitory activity of hibifolin on adenosine deaminase- experimental and molecular modeling study

Adenosine deaminase (ADA) is an enzyme involved in purine metabolism. ADA converts adenosine to inosine and liberates ammonia. Because of their critical role in the differentiation and maturation of cells, the regulation of ADA activity is considered as a potential therapeutic approach to prevent malignant and inflammatory disorders. In the present study, the inhibitory activity of a plant flavonoid, hibifolin on ADA is investigated using enzyme kinetic assay and isothermal titration calorimetry. The inhibitory constant of hibifolin was found to be 49.92 μM ± 3.98 and the mode of binding was reversible. Isothermal titration calorimetry showed that the compound binds ADA with binding energy of −7.21 Kcal/mol. The in silico modeling and docking studies showed that the bound ligand is stabilized by hydrogen bonds with active site residues of the enzyme. The study reveals that hibifolin can act as a potential inhibitor of ADA.     

A thermodynamic model for calculating nitrogen solubility,gas phase composition and density of the N2–H2O–NaCl system

A thermodynamic model is presented to calculate N₂ solubility in pure water (273–590 K and 1–600 bar) and aqueous NaCl solutions (273–400 K, 1–600 bar and 0–6 mol kg⁻¹) with or close to experimental accuracy. This model is based on a semi-empirical equation used to calculate gas phase composition of the H₂O–N₂ system and a specific particle interaction theory for liquid phase. With the parameters evaluated from N₂–H₂O–NaCl system and using a simple approach, the model is extended to predict the N₂ solubility in seawater accurately. Liquid phase density of N₂–H₂O–NaCl system at phase equilibrium and the homogenization pressure of fluid inclusions containing N₂–H₂O–NaCl can be calculated from this model. A computer code is developed for this model and can be downloaded from the website: www.geochem-model.org/programs.htm.     

Exploration of interaction zones of β-tubulin colchicine binding domain of helminths and binding mechanism of anthelmintics

Numerous studies postulated the possible modes of anthelmintic activity by targeting alternate or extended regions of colchicine binding domain of helminth β-tubulin. We present three interaction zones (zones vide −1 to −3) in the colchicine binding domain of Haemonchus contortus (a helminth) β-tubulin homology model and developed zone-wise structure-based pharmacophore models coupled with molecular docking technique to unveil the binding hypotheses. The resulted ten structure-based hypotheses were then refined to essential three point pharmacophore features that captured recurring and crucial non-covalent receptor contacts and proposed three characteristics necessary for optimal zone-2 binding: a conserved pair of H bond acceptor (HBA to form H bond with Asn226 residue) and an aliphatic moiety of molecule separated by 3.75 ± 0.44 Å. Further, an aliphatic or a heterocyclic group distant (11.75 ± 1.14 Å) to the conserved aliphatic site formed the third feature component in the zone-2 specific anthelmintic pharmacophore model. Alternatively, an additional HBA can be substituted as a third component to establish H bonding with Asn204. We discern that selective zone-2 anthelmintics can be designed effectively by closely adapting the pharmacophore feature patterns and its geometrical constraints.     

Thermodynamics of solvation of some small peptides in water at T = 298.15 K

The enthalpies of solution in water, Δ_solH_m, of some small peptides, namely the amides of five N-acetyl substituted amino acids of glycine, l-alanine, l-proline, l-valine, l-leucine and two cyclic anhydrides of glycine and l-sarcosine (diketopiperazines), were measured by isothermal calorimetry at T = (296.84, 306.89, and 316.95) K. The enthalpies of solution at infinite dilution at T = 298.15 K were derived and added to the enthalpies of sublimation, ${\mathrm{\Delta }}_{\mathrm{sub}}{H}_{\mathrm{m}}^{\circ }$, at the same temperature, to obtain the corresponding solvation enthalpies at infinite dilution, ${\mathrm{\Delta }}_{\mathrm{solv}}{H}_{\mathrm{m}}^{\infty }$. Moreover, the partial molar heat capacities at infinite dilution at T = 298.15 K, $C_{p\text{,}2}^{\infty }$, were calculated by adding molar heat capacities of solid small peptides, C_p,m(cr), to the ${\mathrm{\Delta }}_{\mathrm{sol}}{C}_{p\text{,}\mathrm{m}}^{\infty }$ values obtained from our experimental data. CH₂ group contributions, in terms of solvation enthalpy and partial molar heat capacity, were −3.2 kJ · mol⁻¹ and 89.3 J · K⁻¹ · mol⁻¹, respectively, in good agreement with the literature data. Simple additive methods were used to estimate the average molar enthalpy of solvation and partial molar heat capacity at infinite dilution for the 1/2CONH⋯CONH functional group in the small peptides. Values obtained were −46.7 kJ · mol⁻¹ for solvation enthalpy and −42.4 J · K⁻¹ · mol⁻¹ for partial molar heat capacity, significantly lower than values obtained for the CONH functional group in monofunctional model compounds.     

Novel thiosemicarbazones derivatives bearing aromatic iodine moiety: Design,synthesis and anti-malarial activity

A series of thiosemicarbazones of aromatic iodide derivatives were designed and synthesized. The structures of all the newly synthesized compounds had been identified by elemental analysis, ¹H NMR and ¹³C NMR. Their biological activities were evaluated against Plasmodium falciparum. Among these compounds, at concentrations of 3, 9 and 27 mg/kg of mouse per day, 4e inhibited the growth of the malaria parasite in vivo test in mice with the respective percentages: 88.1%, 90.7% and 92.6%. The present work suggest that thiosemicarbazones of aromatic iodide may become a lead compound for anti-malaria medicine.