Identification of new dual spleen tyrosine kinase (Syk) and phosphoionositide-3-kinase δ (PI3Kδ) inhibitors using ligand and structure-based integrated ideal pharmacophore models

Owing to the complex pathophysiology of autoimmune disorders, it is very challenging to develop successful treatment strategies. Single-target agents are not desired therapeutics for such multi-factorial disorders. Considering the current need for the treatment of complex autoimmune disorders, dual inhibitors of Syk and PI3Kδ have been designed using ligand and structure-based molecular modelling strategies. In the present work, structure and ligand-based pharmacophore modelling was implemented for a varied set of Syk and PI3Kδ inhibitors. Ligand-based pharmacophore models (LBPMs) were developed for two kinases: ADPR.14 (r²_train = 0.809) for Syk, comprising one hydrogen bond acceptor, one hydrogen bond donor, one positive ionisable and one ring aromatic feature, and for PI3Kδ: AAARR.45 (r²_train = 0.942) consisting of three hydrogen bond acceptor and two ring aromatic features. The generated e-pharmacophore models revealed an additional ring aromatic and hydrophobic feature important for Syk and PI3Kδ inhibition, respectively. Subsequently, LBPMs were modified resulting in APDRR.14 hypothesis for Syk inhibitors and AAAHRR.45 hypothesis for PI3Kδ inhibitors employed for virtual screening. Thus, the combination of ligand and structure-based pharmacophore modelling helped in developing ideal pharmacophore models that may be an efficient tool for the designing of novel dual inhibitors of Syk and PI3Kδ.     

Pharmacophore modelling and electronic feature analysis of hydroxamic acid derivatives,the HIV integrase inhibitors

Hydroxamic acid derivatives with metal ion binding properties were collected from the literature to generate a pharmacophore and 3D-QSAR model for HIV strand transfer inhibition. The derived pharmacophore model (AAAHRR) recognizes both metal ion binding site and hydrophobic group. The QSAR model generated using this hypothesis expressed statistical significance (r ² = 0.971 for the training set and q ² = 0.913 for the test set). The ability of this pharmacophore model to retrieve other metal ion binding inhibitors was examined by screening the ChemBank database (ligandinfo) incorporated with 10 known strand transfer inhibitors. The studied favourable and unfavourable contours of chemical features (H-bond donor, acceptor and hydrophobic sites) revealed the role of hydrophobic substitution at the fluorobenzene ring and cyclization of the metal ion binding hydroxamic acid in effective integrase inhibition. Analysis of the frontier orbitals, HOMO and LUMO revealed that the nucleophilic / electrophilic interactions depend on the significant overlapping observed at the azaindole and hydroxamic acid groups. In essence, the generated pharmacophore model is competent enough to disclose the essential site-specific interactions involved in the inhibition of HIV integrase, and hence can be used in virtual screening to identify novel scaffolds as leads with increased anti-viral potency.     

Synthesis of p-Nitro-stilbene Derivatives with Different Linking Bonds:An Attempt to Tune Spectroscopy of Dyes with Molecular Engineering

The synthesis, characterization and spectroscopy of a range of novel substituted p‐nitro‐stilbene derivatives with different bridging bonds were presented. The molecular structure characterization was carried out with ¹H NMR, ¹³C NMR and elemental analysis. The ultraviolet/visible spectroscopy and photoluminescence of the compounds were investigated in various solvents. The maximal absorption wavelength of the nitro‐stilbene derivatives with an ether bond exhibited approximate 30 to 40 nm bathochromic shift compared to that of nitro‐stilbene dyes with an ester bond. Furthermore, the nitro‐stilbene derivatives with an ether bond displayed obvious photoluminescence, while the nitro‐stilbene derivatives with an ester bond showed weak fluorescence emission. The detection of the cyclic voltammograms of the nitro‐stilbene derivatives showed that the nitro‐stilbene compounds with different linking bonds exhibited different redox proceses at various scan rates. The theroretical calculations of HOMO and LUMO energy of nitro‐stilbene derivatives showed that the energy gaps between HOMO and LUMO of 3 and 4 were lower than those of 1 and 2 . The electron density of the frontier orbitals of nitro‐stilbene derivatives was observed to be affacted by the linking bonds, which thus made it possible to tune the spectroscopy of these dyes with chemical strategy. The differential scanning calorimetry and thermogravimetry showed that the thermal stabilities of these dyes were not much affected by the linking bond. The results presented in this paper would be great interest in development of ideal nitro‐stilbene derivatives for special purposes.     

Molecular dynamics and pharmacophore modelling studies of different subtype (ALK and EGFR (T790M)) inhibitors in NSCLC

Extensively validated 3D pharmacophore models for ALK (anaplastic lymphoma kinase) and EGFR (T790M) (epithelial growth factor receptor with acquired secondary mutation) were developed. The pharmacophore model for ALK (r² = 0.96, q² = 0.692) suggested that two hydrogen bond acceptors and three hydrophobic groups arranged in 3-D space are essential for the binding affinity of ALK inhibitors. Similarly, the pharmacophore model for EGFR (T790M) (r² = 0.92, q² = 0.72) suggested that the presence of a hydrogen bond acceptor, two hydrogen bond donors and a hydrophobic group plays vital role in binding of an inhibitor of EGFR (T790M). These pharmacophore models allowed searches for novel ALK and EGFR (T790M) dual inhibitors from multiconformer 3D databases (Asinex, Chembridge and Maybridge). Finally, the eight best hits were selected for molecular dynamics simulation, to study the stability of their complexes with both proteins and final binding orientations of these molecules. After molecular dynamics simulations, one hit has been predicted to possess good binding affinity for both ALK and EGFR (T790M), which can be further investigated for its experimental in-vitro/in-vivo activities.     

Identification of novel PfDHODH inhibitors as antimalarial agents via pharmacophore-based virtual screening followed by molecular docking and in vivo antimalarial activity

Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyses the fourth reaction of de novo pyrimidine biosynthesis in parasites, and represents an important target for the treatment of malaria. In this study, we describe pharmacophore-based virtual screening combined with docking study and biological evaluation as a rational strategy for identification of novel hits as antimalarial agents. Pharmacophore models were established from known PfDHODH inhibitors using the GALAHAD module with IC₅₀ values ranging from 0.033 μM to 142 μM. The best pharmacophore model consisted of three hydrogen bond acceptor, one hydrogen bond donor and one hydrophobic features. The pharmacophore models were validated through receiver operating characteristic and Günere–Henry scoring methods. The best pharmacophore model as a 3D search query was searched against the IBS database. Several compounds with different structures (scaffolds) were retrieved as hit molecules. Among these compounds, those with a Q_FIT value of more than 81 were docked in the PfDHODH enzyme to further explore the binding modes of these compounds. In silico pharmacokinetic and toxicities were predicted for the best docked molecules. Finally, the identified hits were evaluated in vivo for their antimalarial activity in a parasite inhibition assay. The hits reported here showed good potential to become novel antimalarial agents.     

Pharmacophore generation of 2-substituted benzothiazoles as AdeABC efflux pump inhibitors in A. baumannii

RND family efflux pumps are important for multidrug resistance in Gram-negative bacteria. To date no efflux pump inhibitors for clinical use have been found, so developing the specific inhibitors of this pump system will be beneficial for the treatment of infections caused by these multidrug-resistant pathogens. A set of BSN-coded 2-substituted benzothiazoles were tested alone and in combination with ciprofloxacin (CIP) against the RND family efflux pump AdeABC overexpressor Acinetobacter baumannii SbMox-2 strain. The results indicated that the BSN compounds did not have antimicrobial activity when tested alone. However, if they were applied in combination with CIP, it was observed that the antibiotic had antimicrobial activity against the tested pathogen, possessing a minimum inhibitory concentration value that could be utilized in clinical treatment. A 3D-common features pharmacophore model was applied by using the HipHop method and the generated pharmacophore hypothesis revealed that the hydrogen bond acceptor property of nitrogen in the thiazole ring and the oxygen of the amide substituted at the second position of the benzothiazole ring system were significant for binding to the target protein. Moreover, three hydrophobic aromatic features were found to be essential for inhibitory activity.     

The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study

β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C−N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a–2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C−N), which is why the six-membered ring lactams C−N bond are more rigid than those with five-membered ring lactams. The calculated ΔG^# values from the acylation reaction of the lactams (involving the S−H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C−N cleavage in the five-membered ring lactams especially in the 1–2 derivatives (17.58 kcal mol⁻¹). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.     

A three-dimensional chemical phase pharmacophore mapping,QSAR modelling and electronic feature analysis of benzofuran salicylic acid derivatives as LYP inhibitors

Lymphoid tyrosine phosphatase (LYP), encoded by the PTPN22 gene, has a critical negative regulatory role in T-cell antigen receptor (TCR) and emerged as a promising drug target for human autoimmune diseases. A five-point pharmacophore with two hydrogen bond acceptors, one hydrogen bond donor and two aromatic ring features was generated for a series of benzofuran salicylic acid derivatives as LYP inhibitors in order to elucidate their anti-autoimmune activity. The generated pharmacophore yielded a significant 3D-QSAR model with r² of 0.9146 for a training set of 27 compounds. The model also showed excellent predictive power with Q² of 0.7068 for a test set of eight compounds. The investigation of the 3D-QSAR model has revealed the structural insights which could lead to more potent analogues. The most active and inactive compounds were further subjected to electronic structure analysis using density functional theory (DFT) at B3LYP/3?21^?G level to support the 3D-QSAR predictions. The results obtained from this study are expected to be useful in the proficient design and development of benzofuran salicylic acid derivatives as inhibitors of LYP.     

N‐Benzylnicotinamide and N‐benzyl‐1,4‐dihydronicotinamide: useful models for NAD+ and NADH

3‐Aminocarbonyl‐1‐benzylpyridinium bromide (N‐benzylnicotinamide, BNA), C₁₃H₁₃N₂O⁺·Br⁻, (I), and 1‐benzyl‐1,4‐dihydropyridine‐3‐carboxamide (N‐benzyl‐1,4‐dihydronicotinamide, rBNA), C₁₃H₁₄N₂O, (II), are valuable model compounds used to study the enzymatic cofactors NAD(P)⁺ and NAD(P)H. BNA was crystallized successfully and its structure determined for the first time, while a low‐temperature high‐resolution structure of rBNA was obtained. Together, these structures provide the most detailed view of the reactive portions of NAD(P)⁺ and NAD(P)H. The amide group in BNA is rotated 8.4 (4)° out of the plane of the pyridine ring, while the two rings display a dihedral angle of 70.48 (17)°. In the rBNA structure, the dihydropyridine ring is essentially planar, indicating significant delocalization of the formal double bonds, and the amide group is coplanar with the ring [dihedral angle = 4.35 (9)°]. This rBNA conformation may lower the transition‐state energy of an ene reaction between a substrate double bond and the dihydropyridine ring. The transition state would involve one atom of the double bond binding to the carbon ortho to both the ring N atom and the amide substituent of the dihydropyridine ring, while the other end of the double bond accepts an H atom from the methylene group para to the N atom.     

A 3D QSAR pharmacophore model and quantum chemical structure--activity analysis of chloroquine(CQ)-resistance reversal

Using CATALYST, a three-dimensional QSAR pharmacophore model for chloroquine(CQ)-resistance reversal was developed from a training set of 17 compounds. These included imipramine (1), desipramine (2), and 15 of their analogues (3-17), some of which fully reversed CQ-resistance, while others were without effect. The generated pharmacophore model indicates that two aromatic hydrophobic interaction sites on the tricyclic ring and a hydrogen bond acceptor (lipid) site at the side chain, preferably on a nitrogen atom, are necessary for potent activity. Stereoelectronic properties calculated by using AM1 semiempirical calculations were consistent with the model, particularly the electrostatic potential profiles characterized by a localized negative potential region by the side chain nitrogen atom and a large region covering the aromatic ring. The calculated data further revealed that aminoalkyl substitution at the N5-position of the heterocycle and a secondary or tertiary aliphatic aminoalkyl nitrogen atom with a two or three carbon bridge to the heteroaromatic nitrogen (N5) are required for potent "resistance reversal activity". Lowest energy conformers for 1-17 were determined and optimized to afford stereoelectronic properties such as molecular orbital energies, electrostatic potentials, atomic charges, proton affinities, octanol-water partition coefficients (log P), and structural parameters. For 1-17, fairly good correlation exists between resistance reversal activity and intrinsic basicity of the nitrogen atom at the tricyclic ring system, frontier orbital energies, and lipophilicity. Significantly, nine out of 11 of a group of structurally diverse CQ-resistance reversal agents mapped very well on the 3D QSAR pharmacophore model.     

Molecular and electronic structures of anionic σ-complexes of 9-nitroanthracene and its derivatives studied byab initio HF/6-31G** calculations

The molecular structures of anionic σ-complexes of 9-nitroanthracene and its 10-methoxy and 10-acetonyl derivatives were calculated by theab initio quantum-chemical HF/6-31G^** method. The central ring of the anthracene fragment adopts a boat conformation. The values of the bond lengths and bond orders in the compounds under study indicate that the contribution of theaci-resonance form to the structure of the nitro group is substantially larger than that estimated for 2,4,6-trinitrobenzene derivatives. The substituents have no substantial effect on the geometry of the anion. The negative charge is localized mainly on the oxygen atoms of the nitro group and of the substituents. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2142–2145, November, 1998.     

Binding mode of inhibitors and Cryptosporidium parvum IMP dehydrogenase: A combined ligand- and receptor-based study

A combined ligand- and target-based approach was used to analyse the interaction models of Cryptosporidium parvum inosine 5’-monophosphate dehydrogenase (CpIMPDH) with selective inhibitors. First, a ligand-based pharmacophore model was generated from 20 NAD⁺ competitive CpIMPDH inhibitors with the HipHop module. The characteristic of the NAD⁺ binding site of CpIMPDH was then described, and the binding modes of the representative inhibitors were studied by molecular docking. The combination of the pharmacophore model and the docking results allowed us to evaluate the pharmacophore features and structural information of the NAD⁺ binding site of CpIMPDH. This research supports the proposal of an interaction model inside the NAD⁺ binding site of CpIMPDH, consisting of four key interaction points: two hydrophobic-aromatic groups, a hydrophobic-aliphatic group and a hydrogen bond donor. This study also provides guidance for the design of more potent CpIMPDH inhibitors for the treatment of Cryptosporidium infections.     

Identification of potential CRAC channel inhibitors: Pharmacophore mapping, 3D-QSAR modelling,and molecular docking approach

Upregulation of store-operated Ca²⁺ influx via ORAI1, an integral component of the CRAC channel, is responsible for abnormal cytokine release in active rheumatoid arthritis, and therefore ORAI1 has been proposed as an attractive molecular target. In this study, we attempted to predict the mechanical insights of ORAI1 inhibitors through pharmacophore modelling, 3D-QSAR, molecular docking and free energy analysis. Various hypotheses of pharmacophores were generated and from that, a pharmacophore hypothesis with two hydrogen bond acceptors, one hydrogen bond donor and two aromatic rings (AADRR) resulted in a statistically significant 3D-QSAR model (r² = 0.84 and q² = 0.74). We believe that the obtained statistical model is a reliable QSAR model for the diverse dataset of inhibitors against the IL-2 production assay. The visualization of contours in active and inactive compounds generated from the 3D-QSAR models and molecular docking studies revealed major interaction with GLN108, HIS113 and ASP114, and interestingly, these residues are located near the Ca²⁺ selectivity filter region. Free energy binding analysis revealed that Coulomb energy, van der Waals energy and non-polar solvation terms are more favourable for ligand binding. Thus, the present study provides the physical and chemical requirements for the development of novel ORAI1 inhibitors with improved biological activity.     

Theoretical investigation on the structures,densities, and detonation properties of polynitrotetraazaoctahydroanthracenes

The polynitrotetraazaoctahydroanthracenes were optimized to obtain their molecular geometries and electronic structures at density functional theory–B3LYP/6‐31+G(d) level. Detonation velocities (D) and detonation pressures (P) were estimated for this nitramine compounds using Kamlet‐Jacobs equations, based on the theoretical densities (ρ) and heats of formation. It is found that there are good linear relationships between volume, density, detonation velocity, detonation pressure and the number of nitro group. Thermal stability of the compounds was investigated by calculating the bond dissociation energies and energy gap (ΔE_LUMO–HOMO). The simulation results reveal that molecule H performs similarly to famous explosive RDX. These results provide basic information for molecular design of novel high energetic density compounds. © 2011 Wiley Periodicals, Inc.     

Synthesis,antitubercular evaluation and molecular docking studies of phthalimide bearing 1,2,3-triazoles

In a search for safer and potent antitubercular agents, here a library of newly substituted dioxoisoindolinylmethyl-triazolyl-N-phenylacetamide derivatives (5a–l) has been synthesized via click chemistry approach. All synthesized compounds were evaluated for their antitubercular activity against Mycobacterium tuberculosis H₃₇Rv (MTB). Among the screened compounds, 5d, 5e, 5h, and 5l showed good antitubercular activity. The compounds 5d and 5l have shown very effective antitubercular activity against Mycobacterium tuberculosis H₃₇Rv (MTB) with MIC 12.5?μg/mL. All the newly synthesized compounds were thoroughly characterized by ¹H NMR, ¹³C NMR, and HRMS spectral data. We further performed exploratory docking studies on the crystal structure of Mycobacterium tuberculosis enoyl reductase to demonstrate the mechanism of antitubercular activity.     

Pharmacophore modelling,virtual screening and molecular docking studies on PLD1 inhibitors

Lipid metabolism plays a significant role in influenza virus replication and subsequent infection. The regulatory mechanism governing lipid metabolism and viral replication is not properly understood to date, but both Phospholipase D (PLD1 and PLD2) activities are stimulated in viral infection. In vitro studies indicate that chemical inhibition of PLD1 delays viral entry and reduction of viral loads. The current study reports a three-dimensional pharmacophore model based on 35 known PLD1 inhibitors. A sub-set of 25 compounds was selected as the training set and the remaining 10 compounds were kept in the test set. One hundred and twelve pharmacophore models were generated; a six-featured pharmacophore model (AADDHR.57) with survival score (2.69) produced a statistically significant three-dimensional quantitative structure–activity relationship model with r² = 0.97 (internal training set), r² = 0.71 (internal test set) and Q² = 0.64. The predictive power of the pharmacophore model was validated with an external test set (r² = 0.73) and a systematic virtual screening work-flow was employed showing an enrichment factor of 23.68 at the top 2% of the dataset (active and decoys). Finally, the model was used for screening of the filtered PubChem database to fetch molecules which can be proposed as potential PLD1 inhibitors for blocking influenza infection.     

Donor‐Acceptor‐Functionalized Tetraethynylethenes with Nitrothienyl Substituents: Structure‐Property Relationships

Tetraethynylethenes (TEEs) functionalized with donor (4‐(dimethylamino)phenyl) and acceptor (5‐nitro‐2‐thienyl) groups were prepared by Pd⁰‐catalyzed Sonogashira cross‐coupling reactions (Schemes 1 – 6). The physical properties of these novel chromophores were examined and compared with those of analogous systems containing 4‐nitrophenyl instead of 5‐nitro‐2‐thienyl acceptor groups. X‐Ray crystal‐structure analyses showed the π‐conjugated frameworks of 2 , 11 , and 13 , including the TEE core and all aryl moieties, to be nearly perfectly planar (Figs. 1, 3, and 4). In contrast, one 4‐(dimethylamino)phenyl group in 10 is rotated almost 90° out of the molecular plane, presumably due to crystal‐packing effects (Fig. 2). The analysis of bond lengths and bond angles revealed little, if any, evidence of intramolecular ground‐state donor‐acceptor interactions. The electrochemical behavior of nitrothienyl‐substituted TEEs is similar to that of the corresponding nitrophenyl‐functionalized derivatives (Table 3). The nitrothienyl groups were reduced at −1.23 V (vs. the ferrocene/ferricinium couple, Fc/Fc⁺), regardless of the degree or pattern of other substitutions. For nonsymmetrical TEE 13 , the reduction of the nitrothienyl group at −1.23 V is followed by a reduction of the nitrophenyl group at −1.40 V, a potential typical for the reduction of other nitrophenyl‐substituted TEEs, such as 17 – 20 . UV/VIS Spectroscopy showed a consistently lower‐energy absorption cutoff for nitrothienyl derivatives compared with the analogous nitrophenyl‐substituted TEEs that confirms a lowering of the HOMO‐LUMO gap as a result of nitrothiophene substitution (Figs. 5 and 6). A comparison of the tetrakis‐arylated TEEs 11 , 13 , and 20 clearly showed a steady bathochromic shift of the longest‐wavelength absorption maximum and the end‐absorption upon sequential replacement of nitrophenyl by nitrothienyl groups. Quantum‐chemical computations were performed to explain a number of complex features of the electronic absorption spectra. All empirical features of relevance in the experimental UV/VIS spectra for 2 , 5 , 6 , and 17 – 19 were correctly reproduced by computation (Tables 4 and 5). The combination of theory and experiment was found to be very useful to explain the particular acceptor properties of the 5‐nitro‐2‐thienyl group.     

Pharmacophore Modeling and Virtual Screening of Novel Inhibitors for c-Kit Kinase

The stem cell factor receptor (c‐Kit) has been known to play critical roles in regulating numerous aspects of cellular behavior including cell growth, differentiation, migration and metabolism. In this investigation, a three‐dimensional pharmacophore model of c‐Kit inhibitors has been established by using the HypoGen algorithms implemented in the catalyst software package. The best quantitative pharmacophore model, hypothesis 1, which has the highest correlation coefficient (0.989), consists of one hydrogen bond acceptor, two hydrogen bond donors and one hydrophobic feature. To our knowledge, this is the first report on the pharmacophore modeling study of c‐Kit inhibitors. The best hypothesis, hypothesis 1, was used to screen molecular structural databases, including Specs and China Natural Products Database for potential lead compounds. The hit compounds were subsequently subjected to filtering by Lipinski's rules and docking study to refine the retrieved hits and as a result to reduce the rate of false positive. Finally 28 compounds were purchased or synthesized for further in vitro assay against several human tumour cell lines including A549, MCF‐7, HepG2 and PC‐3, in which c‐Kit is overexpressed. Two compounds show very low micromolar inhibition potency against the PC‐3 and HepG2 cell lines respectively. And they were selected for further modification and testing.     

Tuning of the electronic properties of H‐passivated armchair graphene nanoribbons by mild border oxidation: Theoretical study on periodic models

We report the results of a DFT study of the electronic properties, intended as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, of periodic models of H‐passivated armchair graphene nanoribbons (a‐GNRs) as that synthetized by bottom‐up technique, functionalized by vicinal dialdehydic groups. This material can be obtained by border oxidation in mild and easy to control conditions with ¹Δ_g O₂ as we reported in our previous paper (Ghigo et al., ChemPhysChem 2015, 16, 3030). The calculations show that the two models of border oxidized a‐GNRs (model A, 0.98 nm and model B, 1.35 nm wide) present LUMO and HOMO energies lowered by an extend roughly linearly dependent on the amount of oxygen chemically bound. The frontier orbital energy variations dependence on the % wt of oxygen bound are, for model A: ?0.12 eV for the LUMO and ?0.05 eV for the HOMO; for model B: ?0.15 eV (HOMO) and ?0.06 eV (LUMO). © 2016 Wiley Periodicals, Inc.     

Comparative pharmacophore modeling of human adenosine receptor A1 and A3 antagonists

Adenosine receptors are promising therapeutic targets in drug discovery. In this study, three-dimensional pharmacophore models of human adenosine receptor A1 and A3 antagonists were developed based on 26 and 23 diverse compounds, respectively. The best A1 pharmacophore model (A 1 _Hopy1) consists of four features: one hydrogen bond donor, one hydrophobic point and two ring aromatics, while the best A 3 pharmacophore model (A3 _Hopy1) also has four features: one hydrogen bond acceptor, one hydrophobic point and two ring aromatics. The correlation coefficients were 0.840 for A 1 test set with 146 diverse compounds and 0.827 for A3 test set with 238 diverse compounds. In the simulated virtual screening experiments, high enrichment factors of 6.51 and 6.90 were obtained for A 1 _Hopy1 and A3 _Hopy1 models, respectively. Moreover, two models also showed high subtype-selectivity in the simulated virtual screening experiments. These results could be helpful for the discovery of novel potent and selective A 1 and A3 antagonists.