Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction

Computational drug design relies on the calculation of binding strength between two biological counterparts especially a chemical compound, i.e., a ligand, and a protein. Predicting the affinity of protein-ligand binding with reasonable accuracy is crucial for drug discovery, and enables the optimization of compounds to achieve better interaction with their target protein. In this paper, we propose a data-driven framework named DeepAtom to accurately predict the protein-ligand binding affinity. With 3D Convolutional Neural Network (3D-CNN) architecture, DeepAtom could automatically extract binding related atomic interaction patterns from the voxelized complex structure. Compared with the other CNN based approaches, our light-weight model design effectively improves the model representational capacity, even with the limited available training data. We carried out validation experiments on the PDBbind v.2016 benchmark and the independent Astex Diverse Set. We demonstrate that the less feature engineering dependent DeepAtom approach consistently outperforms the other baseline scoring methods. We also compile and propose a new benchmark dataset to further improve the model performances. With the new dataset as training input, DeepAtom achieves Pearson's R=0.83 and RMSE=1.23 pK units on the PDBbind v.2016 core set. The promising results demonstrate that DeepAtom models can be potentially adopted in computational drug development protocols such as molecular docking and virtual screening.

Modeling the Effects of Citrus sinensis Essential Oil and Nitrite on Growth Probability of Clostridium botulinum Type A in Broth Media

Background:

Nitrite is a multifunctional food additive used for control of toxigenic Clostridium botulinum in foodstuffs. However, there is a growing concern about the carcinogenic and teratogenic effects of nitrite. The present research was done to assess the effects of Citrus sinensis essential oil and nitrite on the growth probability of C. botulinum type A using predictive mathematical modeling technique in broth media.

Methods:

Essential oil of C. sinensis was collected using Clevenger. Multifactorial design included diverse C. sinensis, nitrite and NaCl concentrations and also different pH ranges and storage temperatures were arranged in BHI broth medium. C. botulinum type A strains were then inoculated and their growth model was analyzed.

Results:

The synergistic inhibitory effects of nitrite and C. sinensis were significant (P<0.05). C. sinensis (0.045%) and nitrite (20 ppm) strongly decreased the growth of C. botulinum (log P%= - 2.2 versus log P%= 1.15). Decreasing temperature up to 25°C significantly affected growth probability of C. botulinum (P<0.05). Increasing NaCl concentration up to 3% did not cause any significant differences in the growth of C. botulinum (P= 0.062). Bacterial growth in broth media was completely inhibited at pH 5.5 and also in media contained C. sinensis (0.045%) and nitrite (60 ppm) at pH 6.5 (log P%= -3.76).

Conclusion:

Using certain concentrations of C. sinensis essential oil with other suboptimal factors (pH and temperature) and nitrite can control the growth of C. botulinum in broth media.

Discovery of Amantamide, a Selective CXCR7 Agonist from Marine Cyanobacteria

CXCR7 plays an emerging role in several physiological processes. A linear peptide, amantamide (1), was isolated from marine cyanobacteria, and the structure was determined by NMR and mass spectrometry. The total synthesis was achieved by solid-phase method. After screening two biological target libraries, 1 was identified as a selective CXCR7 agonist. The selective activation of CXCR7 by 1 could provide the basis for developing CXCR7-targeted therapeutics and deciphering the role of CXCR7 in different diseases.

Discovery, Synthesis, Pharmacological Profiling, and Biological Characterization of Brintonamides A-E, Novel Dual Protease and GPCR Modulators from a Marine Cyanobacterium

Five novel modified linear peptides named brintonamides A-E (1-5) were discovered from a marine cyanobacterial sample collected from Brinton Channel, Florida Keys. The total synthesis of 1-5 in addition to two other structurally related analogues (6 and 7) was achieved, which provided more material to allow rigorous biological evaluation and SAR studies. Compounds were subjected to cancer-focused phenotypic cell viability and migration assays and orthogonal target-based pharmacological screening platforms to identify their protease and GPCR modulatory activity profiles. The cancer related serine protease kallikrein 7 (KLK7) was inhibited to similar extents with an IC50 near 20 μM by both representative members 1 and 4, which differed in the presence or lack of the N-terminal unit. In contrast to the biochemical protease profiling study, clear SAR was observed in the functional GPCR screens, where five GPCRs in antagonist mode (CCR10, OXTR, SSTR3, TACR2) and agonist mode (CXCR7) were modulated by compounds 1-7 to varying extents. Chemokine receptor type 10 (CCR10) was potently modulated by brintonamide D (4) with an IC50 of 0.44 μM. We performed in silico modeling to understand the structural basis underlying the differences in the antagonistic activity among brintonamides toward CCR10. Because of the significance of KLK7 and CCR10 in cancer progression and metastasis, we demonstrated the ability of brintonamide D (4) at 10 μM to significantly target downstream cellular substrates of KLK7 (Dsg-2 and E-cad) in vitro and to inhibit CCL27-induced CCR10-mediated proliferation and the migration of highly invasive breast cancer cells.

Saturated N,X-Heterocyclic Carbenes (X=N, O, S, P, Si, C, and B): Stability, Nucleophilicity, and Basicity

Various saturated five-membered N,X-heterocyclic carbenes (X = N, O, S, P, Si, C, and B) have been studied by ab initio and density functional theory (DFT) methods. The substitutions alter the properties of the reference carbene from the viewpoint of electronic structure, stability, nucleophilicity, and basicity. Our study shows that the oxygen containing carbene (X = O) induces the highest HOMO–LUMO energy gap (ΔEHOMO–LUMO), while carbene with X = N has the widest singlet–triplet energy difference (ΔEs–t). The nucleophilicity of the carbene derivatives increased upon replacement of C, Si, and B, with the effect of the boron substituent being more pronounced. In addition, the basicity of the structure increased for the carbene derivatives with X = C and B with the latter substitution imposing a remarkably higher effect. Moreover, the substitution of boron at the α-position of the carbene increased the nucleophilicity and basicity, while inducing a reduction in the values of ΔEs–t and ΔEHOMO–LUMO.

Single-molecule vibrational spectroscopy and microscopy

Vibrational spectra for a single molecule adsorbed on a solid surface have been obtained with a scanning tunneling microscope (STM). Inelastic electron tunneling spectra for an isolated acetylene (C2H2) molecule adsorbed on the copper (100) surface showed an increase in the tunneling conductance at 358 millivolts, resulting from excitation of the C-H stretch mode. An isotopic shift to 266 millivolts was observed for deuterated acetylene (C2D2). Vibrational microscopy from spatial imaging of the inelastic tunneling channels yielded additional data to further distinguish and characterize the two isotopes. Single-molecule vibrational analysis should lead to better understanding and control of surface chemistry at the atomic level.

Inducing and viewing the rotational motion of a single molecule

Tunneling electrons from the tip of a scanning tunneling microscope were used to induce and monitor the reversible rotation of single molecules of molecular oxygen among three equivalent orientations on the platinum(111) surface. Detailed studies of the rotation rates indicate a crossover from a single-electron process to a multielectron process below a threshold tunneling voltage. Values for the energy barrier to rotation and the vibrational relaxation rate of the molecule were obtained by comparing the experimental data with a theoretical model. The ability to induce the controlled motion of single molecules enhances our understanding of basic chemical processes on surfaces and may lead to useful single-molecule devices.