Software for Predicting Binding Free Energy of Protein-Protein Complexes and Their Mutants.

Protein-protein binding affinity prediction is important for understanding complex biochemical pathways and to uncover protein interaction networks. Quantitative estimation of the binding affinity changes caused by mutations can provide critical information for protein function annotation and genetic disease diagnoses. The binding free energies of protein-protein complexes can be predicted using several computational tools.

Software and Databases for Protein-Protein Docking.

Protein-protein interactions (PPIs) provide valuable insights for understanding the principles of biological systems and for elucidating causes of incurable diseases. One of the techniques used for computational prediction of PPIs is protein-protein docking calculations, and a variety of software has been developed. This chapter is a summary of software and databases used for protein-protein docking.

On Integral INICS Aromaticity of Pyridodiazepine Constitutional Isomers and Tautomers.

The structure, energetics, and aromaticity of c.a. 100 constitutional isomers and tautomers of pyrido[m,n]diazepines (m = 1, 2; n = 2, 3, 4, 5; m ≠ n) were studied at the B3LYP/cc-pVTZ level.

Novel Molecular Targets of Antidepressants.

Antidepressants target a variety of proteins in the central nervous system (CNS), the most important belonging to the family of G-protein coupled receptors and the family of neurotransmitter transporters. The increasing number of crystallographic structures of these proteins have significantly contributed to the knowledge of their mechanism of action, as well as to the design of new drugs. Several computational approaches such as molecular docking, molecular dynamics, and virtual screening are useful for elucidating the mechanism of drug action and are important for drug design.

AHR-dependent genes and response to MTX therapy in rheumatoid arthritis patients.

Methotrexate (MTX) is the first-line therapy for rheumatoid arthritis. Nevertheless, MTX resistance is quite a common issue in clinical practice. There are some premises that aryl hydrocarbon receptor (AhR) gene battery may take part in MTX metabolism.

In Silico Screening for Novel Leucine Aminopeptidase Inhibitors with 3,4-Dihydroisoquinoline Scaffold.

Cancers are the leading cause of deaths worldwide. In 2018, an estimated 18.1 million new cancer cases and 9.

Affinity of fentanyl and its derivatives for the σ-receptor.

Fentanyl and its 11 commercially available derivatives were investigated as to their affinity for the σ receptor. The parent compound is a rather poor binder (IC = 4973 nM), but its close derivatives (benzylfentanyl or -fluorofentanyl) have submicromolar affinities. Modelling provides a structural basis for the observed trends in activity.

Molecular dynamics of fentanyl bound to μ-opioid receptor.

The molecular dynamics simulations of fentanyl complexed with the μ-opioid receptor (μOR) were studied using both inactive 4DKL and active 5C1M opioid receptor crystal structures. Analogous simulations in morphine with or without a ligand were done for comparison. Simulations of the inactive states were carried out in the absence and presence of the Na ion.

Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis.

Interactions of 21 fentanyl derivatives with μ-opioid receptor (μOR) were studied using experimental and theoretical methods. Their binding to μOR was assessed with radioligand competitive binding assay. A uniform set of binding affinity data contains values for two novel and one previously uncharacterized derivative.

Oncotoxic Properties of Serotonin Transporter Inhibitors and 5-HT Receptor Ligands.

The cytotoxic activity of several serotonin transporter (SERT) inhibitors and subtype of serotonin receptor 1A (5-HT receptor) ligands have been examined in androgen-insensitive human PC-3 prostate and neuroblastoma SH-SY5Y cancer cells. Almost all of the studied compounds (except 5-HT receptor agonist (2)-(+)-8-Hydroxy-2-(di--propylamino)tetralin hydrobromide (8-OH-DPAT)) exhibited absolute cytotoxic activity against the examined cancer cells. The compound 4-Fluoro--[2-[4-(7-methoxy-1-naphthalenyl)-1-piperazinyl]ethyl]benzamide hydrochloride (S14506) that showed highest activity against neuroblastoma tumors was the 5-HT receptor agonist (although not alike other 5-HT receptor agonists).

Structural Insights into σ₁ Receptor Interactions with Opioid Ligands by Molecular Dynamics Simulations.

Despite considerable advances over the past years in understanding the mechanisms of action and the role of the σ₁ receptor, several questions regarding this receptor remain unanswered. This receptor has been identified as a useful target for the treatment of a diverse range of diseases, from various central nervous system disorders to cancer. The recently solved issue of the crystal structure of the σ₁ receptor has made elucidating the structure-activity relationship feasible.

Molecular docking studies, biological and toxicity evaluation of dihydroisoquinoline derivatives as potential anticancer agents.

We report a study of a series of isoquinoline derivatives, including their synthesis, in vitro microsomal leucine aminopeptidase (LAP) inhibition and antiproliferative activity on cancer cell lines. Among fourteen tested compounds, one (compound 3b) was determined to have good activity against LAP and significant antiproliferative activity against HL-60 human promyelocytic leukemia, Burkitt's lymphoma Raji, camptothecin resistant CEM/C2 leukemia cells with mutated catalytic site of topoisomerase I, its parental cell line CCRF/CEM and LoVo colon cancer. Its influence on the cell cycle was also observed.

New validated HPLC methodology for the determination of (-)-trans-paroxetine and its enantiomer in pharmaceutical formulations with use of ovomucoid chiral stationary phase.

A new chromatographic method for the enantioseparation and the determination of (-)-trans-paroxetine and (+)-trans-paroxetine has been developed with the aid of amylose ovomucoid-based chiral stationary phase. The method is faster and five times more sensitive than procedures recommended previously: limit of detection and limit of quantification are 5 and 16 ng/mL, respectively [modified (Ferretti et al. in J Chromatogr B 710:157-164, 1998): 20 and 60 ng/mL].

Synthesis of imperatorin analogs and their evaluation as acetylcholinesterase and butyrylcholinesterase inhibitors.

In this study, we synthesized several imperatorin analogs using imperatorin and xanthotoxin as substrates. The anti-cholinesterase activities of all compounds were evaluated in in vitro experiments according to the modified Ellman's method. For each synthesized compound, IC50 values for both enzymes were established.

The new HPLC methodology for the chiral separation of tamsulosin enantiomers on amylose tris(3,5-dimethylphenylcarbamate) stationary phase.

New chromatographic method for the enantioseparation of (R,S)-tamsulosin and the determination of (R)- and (S)-tamsulosin was developed with the aid of amylose tris(3,5-dimethylphenylcarbamate) stationary phase. The method was compared to the known procedure for tamsulosin enantioseparation on cellulose tris(3,5-dimethylphenyl carbamate). Careful validation of both methods allowed to prove advantages of the new procedure: significantly better resolution as well as twice better sensitivity.

Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors.

It is well known that 6-nitroquipazine exhibits about 150-fold higher affinity for the serotonin transporter (SERT) than quipazine and recently we showed quipazine buspirone analogues with high to moderate SERT affinity. Now we have designed and synthesized several 6-nitroquipazine buspirone derivatives. Unexpectedly, their SERT binding affinities were moderate, and much lower than that of the previously studied quipazine buspirone analogues.

Mass-spectrometric studies of new 6-nitroquipazines-serotonin transporter inhibitors.

Six synthesized 6-nitroquipazine derivatives were examined by electron ionization (EI) and electrospray ionization (ESI) mass spectrometry in positive and negative ion mode. The compounds exhibit high affinity for the serotonin transporter (SERT) and belong to a new class of SERT inhibitors. The EI mass spectra registered in negative ion mode showed prominent molecular ions for all the compounds studied.

Novel 4-aryl-pyrido[1,2-c]pyrimidines with dual SSRI and 5-HT1A activity: part 2.

Derivatives of 4-aryl-5,6,7,8-tetrahydro-pyrido[1,2-c]pyrimidine were synthesized. These compounds contain the 3-(4-piperidyl)-1H-indole residue or its 5-methoxy or 2-methyl derivative. In vitro binding tests were performed to determine the affinity of the compounds for the 5-HT(1A) receptor and serotonin transporter (SERT) proteins in the rat brain cortex.

The molecular interactions of buspirone analogues with the serotonin transporter.

A major problem with the selective serotonin reuptake inhibitors (SSRIs) is the delayed onset of action. A reason for that may be that the initial SSRI-induced increase in serotonin levels activates somatodendritic 5-HT(1A) autoreceptors, causing a decrease in serotonin release in major forebrain areas. It has been suggested that compounds combining inhibition of the serotonin transport protein with antagonistic effects on the 5-HT(1A) receptor will shorten the onset time.

A homology model of SERT based on the LeuT(Aa) template.

A human serotonin transporter (SERT) model has been constructed based on the crystal structure of the bacterial homologue of Na(+)/Cl(-)-dependent neurotransmitter transporters from Aquifex aeolicus (LeuT(Aa)). Amino acids in the ligand binding area predicted by ICM pocket finder included Tyr95, Ala96, Asp98, Gly100 (transmembrane helix (TMH) 1), Ala169, Ile172, Ala173, Tyr176 (TMH3), Phe335, Ser336, Gly338, Phe341, Val343 (TMH6), Thr439, Ala441, and Gly442 (TMH8). The present model is an updated working tool for experimental studies on SERT.

Intrinsic activity and comparative molecular dynamics of buspirone analogues at the 5-HT(1A) receptors.

In CNS, the 5-hydroxytryptamine(1A) (5-HT(1A)) receptors exist in two different populations with different behavioural and physiological effects: (1) somatodendritic autoreceptors located pre-synaptically of 5-HT containing neurons and (2) receptors located post-synaptic to 5-HT containing neurons. Clinical studies have shown that 5-HT(1A) partial agonists have anxiolytic properties, while antagonists of pre-synaptical autoreceptors shorten the onset time of selective serotonin reuptake inhibitors (SSRIs). In the present study, the pre- and post-synaptic activity of structural analogues of buspirone was evaluated in animal models.