Ning-Ning Wei

Ligand-Based Virtual Screening Approach Using a New Scoring Function

In this study, we aimed to develop a new ligand-based virtual screening approach using an effective shape-overlapping procedure and a more robust scoring function (denoted by the HWZ score for convenience). The HWZ score-based virtual screening approach was tested against the compounds for 40 protein targets available in the Database of Useful Decoys (DUD; dud.docking.org/jahn/ ), and the virtual screening performance was evaluated in terms of the area under the receiver operator characteristic (ROC) curve (AUC), enrichment factor (EF), and hit rate (HR), demonstrating an improved overall performance compared to other popularly used approaches examined. In particular, the HWZ score-based virtual screening led to an average AUC value of 0.84 ± 0.02 (95% confidence interval) for the 40 targets. The average HR values at the top 1% and 10% of the active compounds for the 40 targets were 46.3% ± 6.7% and 59.2% ± 4.7%, respectively. In addition, the performance of the HWZ score-based virtual screening approach is less sensitive to the choice of the target.

Time-dependent density functional theory study on the electronic excited-state hydrogen-bonding dynamics of 4-aminophthalimide (4AP) in aqueous solution: 4AP and 4AP–(H2O)1,2 clusters

The time‐dependent density functional theory (TDDFT) method has been carried out to investigate the excited‐state hydrogen‐bonding dynamics of 4‐aminophthalimide (4AP) in hydrogen‐donating water solvent. The infrared spectra of the hydrogen‐bonded solute−solvent complexes in electronically excited state have been calculated using the TDDFT method. We have demonstrated that the intermolecular hydrogen bond C O···HO and NH···OH in the hydrogen‐bonded 4AP−(H2O)2 trimer are significantly strengthened in the electronically excited state by theoretically monitoring the changes of the bond lengths of hydrogen bonds and hydrogen‐bonding groups in different electronic states. The hydrogen bonds strengthening in the electronically excited state are confirmed because the calculated stretching vibrational modes of the hydrogen bonding CO, amino NH, and HO groups are markedly red‐shifted upon photoexcitation. The calculated results are consistent with the mechanism of the hydrogen bond strengthening in the electronically excited state, while contrast with mechanism of hydrogen bond cleavage. Furthermore, we believe that the transient hydrogen bond strengthening behavior in electroniclly excited state of chromophores in hydrogen‐donating solvents exists in many other systems in solution.

Time-dependent density functional theory study on the coexistent intermolecular hydrogen-bonding and dihydrogen-bonding of the phenol-H2O-diethylmethylsilane complex in electronic excited states

An intermolecular coexistent hydrogen bond and a dihydrogen bond of a novel phenol-H(2)O-diethylmethylsilane (DEMS) complex in the electronically excited states were studied using the time-dependent density functional theory (TDDFT) method. Frontier molecular orbitals analysis revealed that the S(2) state of the dihydrogen-bonded phenol-H(2)O-DEMS complex is a locally excited state in which only the phenol site is electronically excited. Upon electronic excitation, the O-H and H-Si vibrational modes are red shifted compared with those calculated for the ground state. The O-H and H-Si bonds involved in the dihydrogen bond O-H...H-Si and hydrogen bond O-H...O are longer in the S(2) state than in the ground state. The H...H and H...O distances significantly shorten in the S(2) state. Thus, both the intermolecular dihydrogen bond and the hydrogen bond of the phenol-H(2)O-DEMS complex are stronger in the electronically excited state than in the ground state. In addition, the hydrogen bonding is favorable for the formation of the intermolecular dihydrogen bond in the ground state. However, they are competitive with each other in the electronically excited state.

SABRE: ligand/structure-based virtual screening approach using consensus molecular-shape pattern recognition.

We present an efficient and rational ligand/structure shape-based virtual screening approach combining our previous ligand shape-based similarity SABRE (shape-approach-based routines enhanced) and the 3D shape of the receptor binding site. Our approach exploits the pharmacological preferences of a number of known active ligands to take advantage of the structural diversities and chemical similarities, using a linear combination of weighted molecular shape density. Furthermore, the algorithm generates a consensus molecular-shape pattern recognition that is used to filter and place the candidate structure into the binding pocket. The descriptor pool used to construct the consensus molecular-shape pattern consists of four dimensional (4D) fingerprints generated from the distribution of conformer states available to a molecule and the 3D shapes of a set of active ligands computed using SABRE software. The virtual screening efficiency of SABRE was validated using the Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets. The ligand/structure shape-based similarity SABRE algorithm outperforms several other widely used virtual screening methods which uses the data fusion of multiscreening tools (2D and 3D fingerprints) and demonstrates a superior early retrieval rate of active compounds (EF(0.1%) = 69.0% and EF(1%) = 98.7%) from a large size of ligand database (∼95,000 structures). Therefore, our developed similarity approach can be of particular use for identifying active compounds that are similar to reference molecules and predicting activity against other targets (chemogenomics). An academic license of the SABRE program is available on request.

Time‐dependent density functional theory study on excited‐state dihydrogen bonding OH···HGe of the dihydrogen‐bonded phenol‐triethylgermanium complex

Intermolecular dihydrogen bond OH···HGe in the electronically excited state of the dihydrogen‐bonded phenol–triethylgermanium (TEGH) complex was studied theoretically using time‐dependent density functional theory. Analysis of the frontier molecular orbitals revealed a locally excited S1 state in which only the phenol moiety is electronically excited. In the predicted infrared spectrum of the dihydrogen‐bonded phenol–TEGH complex, the OH stretching vibrational mode shifts to a lower frequency in the S1 state in comparison with that in ground state. The GeH stretching vibrational mode demonstrates a relatively smaller redshift than the OH stretching vibrational mode. Upon electronic excitation to the S1 state, the OH and GeH bonds involved in the dihydrogen bond both get lengthened, whereas the CO bond is shortened. With an increased binding energy, the calculated H···H distance significantly decreases in the S1 state. Thus, the intermolecular dihydrogen bond OH···HGe of the dihydrogen‐bonded phenol–TEGH complex becomes stronger in the electronically excited state than that in the ground state.

TIME-DEPENDENT DENSITY FUNCTIONAL THEORY STUDY ON THE ELECTRONIC EXCITED-STATE HYDROGEN BONDING DYNAMICS OF METHYL ACETATE IN AQUEOUS SOLUTION

The time-dependent density functional theory (TDDFT) method has been carried out to investigate the hydrogen-bonding dynamics of methyl acetate (CH3 CO2CH3) in hydrogen-donating water solvent. The ground-state geometry optimizations, electronic transition energies and corresponding oscillation strengths of the low-lying electronically-excited states for the isolated CH3CO2CH3 and H2O monomers, the hydrogen-bonded CH3CO2CH3-(H2O)1, 2 complexes have been calculated using DFT and TDDFT methods respectively. One intermolecular hydrogen bond C=O⋯H–O is formed between CH3CO2CH3 and one water molecule in CH3CO2CH3-H2O dimer. Meanwhile, in CH3CO2CH3-(H2O)2 trimer, two intermolecular hydrogen bonds C=O⋯H–O are formed between CH3CO2CH3 and two water molecules. By theoretically monitoring the excitation energy changes among the CH3CO2CH3 monomer, the CH3CO2CH3-H2O dimer, and the CH3CO2CH3-(H2O)2 trimer, we have demonstrated interestingly that in some electronically-excited states, the intermolecular hydrogen bonds are strengthened inducing electronic spectral redshifts, while in others weakened with electronic spectral blueshifts. The phenomenon that hydrogen bonds are strengthened in some electronic states while weakened in others can arouse further probe into CH3CO2CH3-(H2O)1, 2 complexes.

Application of the 4D Fingerprint Method with a Robust Scoring Function for Scaffold-Hopping and Drug Repurposing Strategies

Two factors contribute to the inefficiency associated with screening pharmaceutical library collections as a means of identifying new drugs: [1] the limited success of virtual screening (VS) methods in identifying new scaffolds; [2] the limited accuracy of computational methods in predicting off-target effects. We recently introduced a 3D shape-based similarity algorithm of the SABRE program, which encodes a consensus molecular shape pattern of a set of active ligands into a 4D fingerprint descriptor. Here, we report a mathematical model for shape similarity comparisons and ligand database filtering using this 4D fingerprint method and benchmarked the scoring function HWK (Hamza–Wei–Korotkov), using the 81 targets of the DEKOIS database. Subsequently, we applied our combined 4D fingerprint and HWK scoring function VS approach in scaffold-hopping and drug repurposing using the National Cancer Institute (NCI) and Food and Drug Administration (FDA) databases, and we identified new inhibitors with different scaffolds of MycP1 protease from the mycobacterial ESX-1 secretion system. Experimental evaluation of nine compounds from the NCI database and three from the FDA database displayed IC50 values ranging from 70 to 100 μM against MycP1 and possessed high structural diversity, which provides departure points for further structure–activity relationship (SAR) optimization. In addition, this study demonstrates that the combination of our 4D fingerprint algorithm and the HWK scoring function may provide a means for identifying repurposed drugs for the treatment of infectious diseases and may be used in the drug-target profile strategy.

A novel and efficient ligand-based virtual screening approach using the HWZ scoring function and an enhanced shape-density model

In this work, we extend our previous ligand shape-based virtual screening approach by using the scoring function Hamza–Wei–Zhan (HWZ) score and an enhanced molecular shape-density model for the ligands. The performance of the method has been tested against the 40 targets in the Database of Useful Decoys and compared with the performance of our previous HWZ score method. The virtual screening results using the novel ligand shape-based approach demonstrated a favorable improvement (area under the receiver operator characteristics curve AUC = .89 ± .02) and effectiveness (hit rate HR1% = 53.0% ± 6.3 and HR10% = 71.1% ± 4.9). The comparison of the overall performance of our ligand shape-based method with the highest ligand shape-based virtual screening approach using the data fusion of multi queries showed that our strategy takes into account deeper the chemical information of the set of active ligands. Furthermore, the results indicated that our method are suitable for virtual screening and yields superior prediction accuracy than the other study derived from the data fusion using five queries. Therefore, our novel ligand shape-based screening method constitutes a robust and efficient approach to the 3D similarity screening of small compounds and open the door to a whole new approach to drug design by implementing the method in the structure-based virtual screening.

Time-dependent density functional theory study of the excited-state dihydrogen bonding: clusters of 2-pyridone with diethylmethylsilane and triethylgermanium

Density functional theory (DFT) was carried out to identify the existence of intermolecular dihydrogen bonds of the 2-pyridone (2PY)-diethylmethylsilane (DEMS) and 2PY-triethylgermanium (TEGH) clusters in the ground state. The H···H distances of both clusters are shorter than the sum of their van der Waals radii. Thus, intermolecular dihydrogen bonds N–H•••H–Si and N–H•••H–Ge exist in the 2PY-DEMS and 2PY-TEGH clusters, respectively. Based on the ground-state conformations, intermolecular dihydrogen bonds N–H•••H–Si and N–H•••H–Ge in the electronically excited state of the 2PY-DEMS and 2PY-TEGH clusters were also investigated using time-dependent density functional theory (TDDFT). Electronic transition of the 2PY-DEMS cluster resembles that of the 2PY-TEGH cluster. Their S1 state is a locally excited (LE) state centered on 2PY moiety. The H•••H distances of the 2PY-DEMS and 2PY-TEGH clusters both stretch in the S1 state compared to those in the ground state. Upon electronic excitation, intermolecular dihydrogen bonding N–H•••H–Si and N–H•••H–Ge can weaken with decreasing dihydrogen bonding energies.

Protein flexibility and conformational states of Leishmania antigen eIF-4A: identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling

Recent homology modeling studies have identified specific residues (epitope) of the Leishmania RNA helicase protein (LmeIF) that stimulates production of IL-12 cytokine. However, question remains concerning how LmeIF’s N-terminal moiety initiates adjuvant effects. Extensive molecular modeling combining the normal mode analysis (NMA) and molecular dynamics simulations, in the present study, has demonstrated that the LmeIF structure may exist in two different forms corresponding to the extended and collapsed (closed) states of the entire structure. The computational results showed that the two domains of the LmeIF structure tend to undergo large fluctuations in a concerted fashion and have strong effect on the solvent accessible surface of the epitope situated on the N-terminal structure. The conformational freedom of the C-terminal domains may explain why the entire LmeIF protein is not as active as the N-terminal moiety. Thereafter, a comparative genome analysis with subsequent homology modeling and molecular electrostatic potential (MEP) techniques allowed us to predict a novel and plausible RNA helicase (LI-helicase) from the Listeria source with adjuvant property as observed for the Leishmania eIF-4A protein. The structural folding and MEP maps revealed similar topologies of the epitope of both LmeIF and LI-helicase proteins and striking identity in the local disposition of the charged groups. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:7