Anti-leishmanial activity of disubstituted purines and related pyrazolo[4,3-d]pyrimidines

We report here results of screening directed to finding new anti-leishmanial drugs among 2,6-disubstituted purines and corresponding 3,7-disubstituted pyrazolo[4,3-d]pyrimidines. These compounds have previously been shown to moderately inhibit human cyclin-dependent kinases. Since some compounds reduced viability of axenic amastigotes of Leishmania donovani, we screened them for interaction with recombinant leishmanial cdc-2 related protein kinase (CRK3/CYC6), an important cell cycle regulator of the parasitic protozoan. Eighteen pairs of corresponding isomers were tested for viability of amastigotes and for inhibition of CRK3/CYC6 kinase activity. Some compounds (9A, 12A and 13A) show activity against amastigotes with EC50 in a range 1.5–12.4 μM. Structure–activity relationships for the tested compounds are discussed and related to the lipophilicity of the compounds

Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines

We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R(2) = 0.49). However, the addition of the active-site waters resulted in significant improvement (R(2) = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors

Effect of physical aging on the gas transport and sorption in PIM-1 membranes

Understanding of the properties over long time scales is a key requirement for the successful application of novel polymers as membrane materials. In this light, the physical aging of dense PIM-1 films with different previous histories was monitored for more than 4 years via parallel gas sorption and permeability measurements. The effect of aging on the individual transport parameters, permeability, solubility and diffusivity, was studied on alcohol treated membranes with high excess free volume. Thermal conditioning of these membranes led to accelerated aging and a reduction of the initial gas permeability and diffusivity of the membranes. A long-term CO2 sorption analysis showed aging affected the sorption kinetics much more than the total equilibrium sorption. This was confirmed by permeation studies with six different gases, showing that the reduction of the permeability coefficient of the samples as a function of time is almost entirely due to a reduction of the diffusion coefficient. A renewed alcohol treatment of the aged membrane led to significant rejuvenation of the membrane. To the best of our knowledge, this is the first systematic long term aging study on PIM-1 via simultaneous analysis of sorption and permeation kinetics. Mixed gas permeation measurements with a CO2/CH4 mixture and an N-2/O-2/CO2 mixture confirm the excellent permselective properties of the PIM-1 membranes even after long aging

Výzkum‚ vývoj a implementace nových měřících metod pro hodnocení znečištění ovzduší a využití v rámci legislativy ES

Projekt byl zaměřen na měření polutantů pomocí pasivních samplerů a modelování rozptylu "nových znečišťujících látek" zejména v městských aglomeracích. Podkladové materiály obsahují závěrečné zprávy za jednotlivé dílčí projekty. DP 1 - Vývoj a aplikace nových měřicích metod. DP 2 - Inovace a doplnění souboru modelů pro rozptylové studie dle direktiv EU a zákona, DP 3 - Vývoj a aplikace Eulerovského modelu

Computational study and peptide inhibitors design for the CDK9 – cyclin T1 complex

Cyclin dependent kinase 9 (CDK9) is a protein that belongs to the cyclin-dependent kinases family, and its main role is in the regulation of the cell transcription processes. Since the increased activity of CDK9 is connected with the development of pathological processes such as tumor growth and survival and HIV-1 replication, inhibition of the CDK9 could be of particular interest for treating such diseases. The activation of CDK9 is initiated by the formation of CDK9/cyclin T1 complex, therefore disruption of its formation could be a promising strategy for the design of CDK9 inhibitors. In order to assist in the design of potential inhibitors of CDK9/cyclin T1 complex formation, a computational study of the CDK9/cyclin T1 interface was conducted. Ten peptides were designed using the information from the analysis of the complex, hot spot residues and fragment based design. The designed peptides were docked to CDK9 structures obtained by molecular dynamics simulations of CDK9/cyclin T1 complex and the CDK9 alone and their binding affinities were evaluated using molecular mechanics Poisson Boltzman surface area (MM-PBSA) method and steered molecular dynamics (SMD). Designed peptide sequences LQTLGF and ESIILQ, both derived from the surface of cyclin T1, as well as the peptide sequence PRWPE, derived from fragment based design, showed the most favorable binding properties and were selected for our further studies