Docking and DFT Studies to explore the Topoisomerase II ATP Pocket employing 3-Substituted 2,6-Piperazindiones for drug design

Synthesis, docking study and inhibitory activity of 2,6-diketopiperazines derived from α-amino acids on HDAC8

Diketopiperazines (DKPs) have been regarded as an important scaffold from the viewpoint of synthesis due to their biological properties for the treatment of several diseases, including cancer. In this work, two novel series of enantiomeric 2,6-DKPs derived from α-amino acids were synthesized through nucleophilic substitution and intramolecular cyclization reactions. All the compounds were docked against histone deacetylase 8 (HDAC8), which is a promising target for the development of anticancer drugs. These compounds bound into the active site of HDAC8 in a similar way to Trichostatin A (TSA), which is an HDAC8 inhibitor. This study showed that the conformation of the 2,6-DKP ring, stereochemistry, and the type of substituent on the chiral center had an important role in the binding modes. The Gibbs free energies and dissociation constants values of HDAC8-ligand complexes showed that compounds (S)-4hBn, (S)-4m, (R)-4h, and (R)-4m were more stable and affine towards HDAC8 than TSA. The inhibitory activities of 4a, (S)-4h, (S)- and (R)-4(g, l, m) were evaluated in vitro on HDAC8. It was found that compounds (R)-4g (IC₅₀ = 21.54 nM) and (R)-4m (IC₅₀ = 10.81 nM) exhibited better inhibitory activities than TSA (IC₅₀ = 28.32 nM). These results suggested that 2,6-DKPs derivatives may be promising anticancer agents for further biological studies.

Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective

Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be drawn. Moreover, users don't always consider sufficient diversity in their test sets which results in certain programs to outperform others. In this review, the prime focus has been laid on the challenges of docking and troubleshooters in existing programs, underlying algorithmic background of docking, preferences regarding the use of docking programs for best results illustrated with examples, comparison of performance for existing tools and algorithms, state of art in docking, recent trends of diseases and current drug industries, evidence from clinical trials and post-marketing surveillance are discussed. These aspects of the molecular drug designing paradigm are quite controversial and challenging and this review would be an asset to the bioinformatics and drug designing communities.

Effect of hydrophobic and hydrogen bonding interactions on the potency of ß-alanine analogs of G-protein coupled glucagon receptor inhibitors

G-protein coupled glucagon receptors (GCGRs) play an important role in glucose homeostasis and pathophysiology of Type-II Diabetes Mellitus (T2DM). The allosteric pocket located at the trans-membrane domain of GCGR consists of hydrophobic (TM5) and hydrophilic (TM7) units. Hydrophobic interactions with the amino acid residues present at TM5, found to facilitate the favorable orientation of antagonist at GCGR allosteric pocket. A statistically robust and highly predictive 3D-QSAR model was developed using 58 β-alanine based GCGR antagonists with significant variation in structure and potency profile. The correlation coefficient (R² ) and cross-validation coefficient (Q² ) of the developed model were found to be 0.9981 and 0.8253, respectively at the PLS factor of 8. The analysis of the favorable and unfavorable contribution of different structural features on the glucagon receptor antagonists was done by 3D-QSAR contour plots. Hydrophobic and hydrogen bonding interactions are found to be main dominating non-bonding interactions in docking studies. Presence of highest occupied molecular orbital (HOMO) in the polar part and lowest unoccupied molecular orbital (LUMO) in the hydrophobic part of antagonists leads to favorable protein-ligand interactions. Molecular mechanics/generalized born surface area (MM/GBSA) calculations showed that van der Waals and nonpolar solvation energy terms are crucial components for thermodynamically stable binding of the inhibitors. The binding free energy of highly potent compound was found to be -63.475 kcal/mol; whereas the least active compound exhibited binding energy of -41.097 kcal/mol. Further, five 100 ns molecular dynamics simulation (MD) simulations were done to confirm the stability of the inhibitor-receptor complex. Outcomes of the present study can serve as the basis for designing improved GCGR antagonists.

Computational insights into factor affecting the potency of diaryl sulfone analogs as Escherichia coli dihydropteroate synthase inhibitors

Dihydropteroate synthase (DHPS) is an alluring target for designing novel drug candidates to prevent infections caused by pathogenic Escherichia coli strains. Diaryl Sulfone (SO) compounds are found to inhibit DHPS competitively with respect to the substrate pABA (p-aminobenzoate). The extra aromatic ring of diaryl sulfone compounds found to stabilize them in highly flexible pABA binding loops. In this present study, a statistically significant 3D-QSAR model was developed using a data set of diaryl sulfone compounds. The favourable and unfavourable contributions of substitutions in sulfone compounds were illustrated by contour plot obtained from the developed 3D-QSAR model. Molecular docking calculations were performed to investigate the putative binding mode of diaryl sulfone compounds at the catalytic pocket. DFT calculations were carried out using SCF approach, B3LYP- 6-31 G (d) basis set to compute the HOMO, LUMO energies and their respective location at pABA binding pocket. Further, the developed model was validated by FEP (Free Energy Perturbation) calculations. The calculated relative free energy of binding between the highly potent and less potent sulfone compound was found to be -3.78 kcal/ mol which is comparable to the experimental value of -5.85 kcal/mol. A 10 ns molecular dynamics simulation of inhibitor and DHPS confirmed its stability at pABA catalytic site. Outcomes of the present work provide deeper insight in designing novel drug candidates for pathogenic Escherichia coli strains.

Interaction of Tamoxifen Analogs With the Pocket Site of Some Hormone Receptors. A Molecular Docking and Density Functional Theory Study

In this paper, the antiestrogenic properties of Tamoxifen analogs have been investigated and a theoretical report of its analogs interaction with the pocket site of some hormone receptors are presented. Analogs were generated by modification of the hydrophilic functional group of Tamoxifen by hydroxyl, amide, carboxyl, and sulfhydryl functional groups, in an attempt to improve their activity and selectivity. The analogs exhibit a negative binding energy in the estrogen and progesterone receptors, which indicates a spontaneous interaction between the analogs and the pocket site in the hormone receptors. The values of the molecular polar surface area indicate that the analogs have good permeability and are strong electrophiles. The couplings showed electrostatic interactions such as hydrogen bond and π-π interactions. According with the Lipinsky Rule of Five, the four analogs presented a good biodistribution, permeability, and pharmacological action on the hormone receptors. The analysis of the charge transfer suggests a limited enhanced oxidative damage in the estrogen receptor that not takes place with the progesterone receptor.