Pharmacophore based virtual screening, molecular docking and biological evaluation to identify novel PDE5 inhibitors with vasodilatory activity

In-silico Studies and Biological Activity of Potential BACE-1 Inhibitors

BACKGROUND

Alzheimer's disease is a neurological condition causing cognitive inability and dementia. The pathological lesions and neuronal damage in the brain are caused by self-aggregated fragments of mutated Amyloidal precursor protein (APP).

OBJECTIVE

The controlled APP processing by inhibition of secretase is the strategy to reduce Aβ load to treat Alzheimer's disease.

METHODS

A QSAR study was performed on 55 Pyrrolidine based ligands as BACE-1 inhibitors with an activity magnitude greater than 4 of compounds.

RESULTS

In the advent of designing new BACE-1 inhibitors, the pharmacophore model with correlation (r = 0.90) and root mean square deviation (RMSD) of 0.87 was developed and validated. Further, the hits retrieved by the in-silico approach were evaluated by docking interactions.

CONCLUSION

Two structurally diverse compounds exhibited Asp32 and Thr232 binding with the BACE-1 receptor. The aryl-substituted carbamate compound exhibited the highest fit value and docking score. The biological activity evaluation by in-vitro assay was found to be >0.1μM.

Identification of Novel Rho-Kinase-II Inhibitors with Vasodilatory Activity

Small GTPase protein Rho-kinase (ROCK) plays an important role in the pathogenesis of hypertension. Inhibition of ROCK II brings about the biochemical changes leading to vascular smooth muscles relaxation, finally resulting into potent antihypertensive activity. In the quest for potent ROCK-II inhibitors, a ligand-based pharmacophore containing four essential chemical features, namely two hydrogen bond acceptor (HBA), one hydrogen bond donor (HBD), and one hydrophobe (HY), was developed and rigorously validated. The pharmacophore was used for virtual screening, and hits retrieved from the National Cancer Institute (NCI) database were sorted on the basis of fit value, estimate value, and Lipinski's violation. Potential feature interaction of hits was also observed during docking studies with the amino acids present in the active site of Rho-kinase. Based on the above screening, three hits (NSC 2488, NSC 2888, and NSC 4231) were chosen and subjected to in vitro Rho-kinase enzyme-based assay, followed by ex vivo rat aortic vasodilatory assay. All three compounds showed good biological activity as predicted by the model and confirmed by the docking studies.

Pharmacophore-driven identification of N-methyl-D-receptor antagonists as potent neuroprotective agents validated using in vivo studies

Alzheimer's disease (AD), apparently the most widespread reason behind dementia, is delineated by a continuous cognitive weakening in the aged. During its progression, N-methyl-D-aspartate receptor (NMDAR) antagonists are known to play a pivotal part in the mechanisms of learning and memory. Since there is an unmet medical need for the treatment of AD, we aim to identify possible chemical compounds targeted toward N-methyl-D-aspartate receptors. Three-dimensional models are developed to unveil some of the essential characteristics of the N-methyl-D-aspartate receptors by using a collection of already discovered N-methyl-D-aspartate receptor inhibitors. This is followed by virtual screening, which results in novel chemical compounds having the potential to inhibit N-methyl-D-aspartate receptors. Molecular docking studies and analysis promulgated two lead compounds with a high LibDock score. The compounds are shortlisted based on high estimated activity, fit values, LibDock score, no violation of Lipinski's, and availability for procuring. Finally, the shortlisted compounds are tested by employing in vivo studies, which we further propose as potential NMDA inhibitors for treating AD.

Investigation of the interaction of a polyamine-modified flavonoid with bovine serum albumin (BSA) by spectroscopic methods and molecular simulation

The interaction between BSA and compound 1 was studied by UV-vis, fluorescence and circular dichroism spectroscopy under physiological conditions (pH = 7.4). Molecular docking and molecular dynamics analyses were also performed. The results showed that compound 1 could bind to BSA. When compound 1 bound to BSA, there were a series of changes in the spectral properties of BSA, which were an enhancement effect of the UV-Vis spectrum of BSA, fluorescence quenching and a weak conformational change in the CD spectrum. The results of the fluorescence experiments at 298, 303 and 310 K showed that fluorescence quenching caused by the addition of compound 1 to BSA was generally static quenching accompanied by a dynamic quenching process, which was shown by the quenching constants of 2.010 × 10⁴ L∙M^-1, 1.850 × 10⁴ L∙M^-1, and 1.970 × 10⁴ L∙M^-1 at the three different temperatures, respectively. From the obtained binding constants and thermodynamic parameters, it was found that hydrophobic forces played an important role in the binding process of 1 to BSA. The results of synchronous fluorescence and three-dimensional fluorescence showed that compound 1 caused a weak conformational change in BSA. Docking results showed that compound 1 was located at binding site II of bovine serum albumin protease. In addition, the flavonoid moiety of compound 1 contributes to the hydrophobic binding of compound 1 to BSA. The results of molecular dynamics, including the root-mean-square deviation (RMSD) and RMS fluctuation (RMSF) values, showed that the binding of compound 1 to BSA did not cause a significant conformational change in BSA.

Discovery of Novel TASK-3 Channel Blockers Using a Pharmacophore-Based Virtual Screening

TASK-3 is a two-pore domain potassium (K_2P) channel highly expressed in the hippocampus, cerebellum, and cortex. TASK-3 has been identified as an oncogenic potassium channel and it is overexpressed in different cancer types. For this reason, the development of new TASK-3 blockers could influence the pharmacological treatment of cancer and several neurological conditions. In the present work, we searched for novel TASK-3 blockers by using a virtual screening protocol that includes pharmacophore modeling, molecular docking, and free energy calculations. With this protocol, 19 potential TASK-3 blockers were identified. These molecules were tested in TASK-3 using patch clamp, and one blocker (DR16) was identified with an IC₅₀ = 56.8 ± 3.9 μM. Using DR16 as a scaffold, we designed DR16.1, a novel TASK-3 inhibitor, with an IC₅₀ = 14.2 ± 3.4 μM. Our finding takes on greater relevance considering that not many inhibitory TASK-3 modulators have been reported in the scientific literature until today. These two novel TASK-3 channel inhibitors (DR16 and DR16.1) are the first compounds found using a pharmacophore-based virtual screening and rational drug design protocol.

Insight into the delivery channel and selectivity of multiple binding sites in bovine serum albumin towards naphthalimide-polyamine derivatives

Naphthalimide derivatives are types of small-molecule anticancer drug candidates; however, their negative factors and potential side effects make their application limited. The pharmacophores select a direct access into the tumor cells as the first choice; this can reduce the side effect of the anti-cancer drugs on the normal cells. Herein, the delivery and binding of the naphthalimide-polyamine complex assisted by the bovine serum albumin (BSA) protein have been studied by combining several molecular dynamic simulations. The plausible transportation channels and the most favorable pathways for the delivery of the naphthalimide-polyamine complex to two drug sites (DSI and DSII), their thermodynamic and dynamic properties and the mechanisms have been discussed in detail. The residues His287 and Phe394 acted as guards in the DSI and DSII, respectively, which played a gating-switch role by flipping the ring from open to close during the compound delivery. The binding mode, binding energy and substituent effects have been also identified. The two drug sites have different preferences towards the compound with the electron-withdrawing and electron-donating substituents, and their strong interactions are more sensitive to the number of the substituent groups. The naphthalimide-polyamine complexes are more likely to choose DSI, both thermodynamically and dynamically, as compared to DSII. This selective specificity of these two drug sites manipulated by the electron-withdrawing and electron-donating substituents is quite promising for the design of new naphthalimide drugs.

Designing modified polybrominated diphenyl ether BDE-47, BDE-99, BDE-100, BDE-183, and BDE-209 molecules with decreased estrogenic activities using 3D-QSAR, pharmacophore models coupled with resolution V of the 210-3 fractional factorial design and molecular docking

A 3D-QSAR model was constructed to predict polybrominated diphenyl ether (PBDE) estrogenic activities expressed as median effective concentrations (pEC₅₀), and resolution V of the 2^10-3 fractional factorial design and a pharmacophore model were used to modify the target PBDE molecules BDE-47, BDE-99, BDE-100, BDE-183, and BDE-209 to decrease the estrogenic activities. The persistent-organic-pollutant-related and flame-retardant properties of the modified molecules were evaluated. The mechanisms involved in decreasing PBDE estrogenic activities were explored through molecular docking. The 3D-QSAR model gave a cross-validated correlation coefficient (q²) of 0.682 (i.e., >0.5) and a non-cross-validated correlation coefficient (r²) of 0.980 (i.e., >0.9). Mono- and di-substitutions and hydrophobic substituent groups gave 40 modified molecules with decreased estrogenic activities, including modified BDE-47 and BDE-99 with pEC₅₀ decreased by >10% and modified BDE-100, BDE-183, and BDE-209 with pEC₅₀ decreased by >20%. The modified molecules had similar flame-retardancy to the unmodified molecules, and lower biotoxicities (by a maximum of 17.27%), persistences (by a maximum of 55.68%), bioconcentration (by 4.28%-23.91%), and long-range transport potentials (by 0.72%-18.47%). Docking indicated that hydrophobic interactions were the main factors affecting PBDE estrogenic activities. The results provide a theoretical basis for designing less estrogenic flame retardants than are currently available.

In silico screening of anthraquinones from Prismatomeris memecyloides as novel phosphodiesterase type-5 inhibitors (PDE-5Is)

OBJECTIVE

Prismatomeris memecyloides Craib (Rubiaceae) is a medicinal plant traditionally used by ethnic minorities in Vietnam for the treatment of erectile dysfunction (ED). The aim of this study was to investigate the chemical compositions and screen in silico its possible inhibitory effect against PDE-5 which reduced cyclic guanosine-3',5'-monophosphate (cGMP) levels and indirectly caused the male ED.

METHODS

Separation of natural compounds were carried out on chromatographic column with silica gel or reversed phase materials, eluting with different solvent gradients. The structures of all isolated compounds were elucidated on the basis of spectroscopic data (HR-MS, 1D/2D-NMR). Docking simulation study of compound (1-7) was performed by using flexible side chains protocol based on Iterated Local Search Global Optimizer Algorithm of AutoDock/Vina v.1.1.2. Pharmacokinetic parameters and toxicity prediction were also calculated by appropriate softwares.

RESULTS

From the methanol extract of roots of P. memecyloides collected in Vietnam, seven compounds including four anthraquinone/one anthraquinone glycoside namely damnacanthal (1), lucidin-ω-methyl ether (2), 3-methylalizarin (3), rubiadin-3-methyl ether (4), and 1-O-methylrubiadin 3-O-primeveroside (5) along with two iridoid glucosides, asperulosidic acid (6) and aitchisonide A (7) were isolated. The molecular modeling results showed that 5 anthraquinone compounds possess the lowest binding energies to PDE-5. The anthraquinone glucoside 1-O-methylrubiadin 3-O-primeveroside (5) potentially inhibited PDE-5 similarly to commercial PDE-5Is sildenafil (SLD) and tadalafil (TLD). Calculated pharmacokinetic results like pIC_50,pred; miLogP, TPSA, enzyme inhibitory of anthraquinone glucoside (5) were similar and even higher to those of the commercial PDE-5 inhibitors. Especially the predictive toxicity of 1-O-methylrubiadin 3-O-primeveroside (5) was even lower than those of SLD and TLD.

CONCLUSION

This is the first study to find a scientific-based evidence for the ethnic use of P. memecyloides as medicinal plant for the treatment of ED. The result indicates that the anthraquinones (damnacanthal (1), lucidin-ω-methyl ether (2), 3-methylalizarin (3) and rubiadin-3-methyl ether (4)), especially anthraquinone glycoside (1-O-methylrubiadin 3-O-primeveroside (5)) are compounds of potential novel drug class for the ED treatment.

Discovery of Novel Soluble Epoxide Hydrolase Inhibitors as Potent Vasodilators

In view of the role of sEH (soluble epoxide hydrolase) in hypertension, we have developed a rigorously validated pharmacophore model containing one HBA (Hydrogen Bond Acceptor), two HY (Hydrophobic) and one RA (Ring Aromatic) features. The model was used as a query to search the NCI (National Cancer Institute) and Maybridge database leading to retrieval of many compounds which were sorted on the basis of predicted activity, fit value and Lipinski’s violation. The selected compounds were docked into the active site of enzyme soluble epoxide hydrolase. Potential interactions were observed between the features of the identified hits and the amino acids present in the docking site. The three selected compounds were subjected to in vitro evaluation using enzyme- based assay and the isolated rat aortic model followed by cytotoxicity studies. The results demonstrate that the identified compounds are potent, safe and novel soluble epoxide hydrolase inhibitors.

Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches, molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development

The essential biological function of phosphodiesterase (PDE) type enzymes is to regulate the cytoplasmic levels of intracellular second messengers, 3′,5′-cyclic guanosine monophosphate (cGMP) and/or 3′,5′-cyclic adenosine monophosphate (cAMP). PDE targets have 11 isoenzymes. Of these enzymes, PDE5 has attracted a special attention over the years after its recognition as being the target enzyme in treating erectile dysfunction. Due to the amino acid sequence and the secondary structural similarity of PDE6 and PDE11 with the catalytic domain of PDE5, first-generation PDE5 inhibitors (i.e. sildenafil and vardenafil) are also competitive inhibitors of PDE6 and PDE11. Since the major challenge of designing novel PDE5 inhibitors is to decrease their cross-reactivity with PDE6 and PDE11, in this study, we attempt to identify potent tadalafil-like PDE5 inhibitors that have PDE5/PDE6 and PDE5/PDE11 selectivity. For this aim, the similarity-based virtual screening protocol is applied for the “clean drug-like subset of ZINC database” that contains more than 20 million small compounds. Moreover, molecular dynamics (MD) simulations of selected hits complexed with PDE5 and off-targets were performed in order to get insights for structural and dynamical behaviors of the selected molecules as selective PDE5 inhibitors. Since tadalafil blocks hERG1 K channels in concentration dependent manner, the cardiotoxicity prediction of the hit molecules was also tested. Results of this study can be useful for designing of novel, safe and selective PDE5 inhibitors.

Analysis of positions and substituents on genotoxicity of fluoroquinolones with quantitative structure-activity relationship and 3D Pharmacophore model

The genotoxicity values of 21 quinolones were studied to establish a quantitative structure-activity relationship model and 3D Pharmacophore model separately for screening essential positions and substituents that contribute to genotoxicity of fluoroquinolones (FQs). A full factor experimental design was performed to analyze the specific main effect and second-order interaction effect of different positions and substituents on genotoxicity, forming a reasonable modification scheme which was validated on typical FQ with genotoxicity and efficacy data. Four positions (1, 5, 7, 8) were screened finally to form the full factorial experimental design which contained 72 congeners in total, illustrating that: the dominant effect of 5 and 7-positions on genotoxicity of FQs is main effect; meanwhile the effect of 1 and 8-positions is a second-order interaction effect; two adjacent positions always have stronger second-order interaction effect and lower genotoxicity; the obtained modification scheme had been validated on typical FQ congeners with the modified compound has a lower genotoxicity, higher synthesis feasibilities and efficacy.

Design, synthesis, molecular modeling and anti-hyperglycemic evaluation of novel quinoxaline derivatives as potential PPARγ and SUR agonists

In our effort to develop potent anti-hyperglycemic agents with potential agonistic activities toward PPARγ and SUR, three novel series of quinoxaline derivatives bearing sulfonylurea or sulfonylthiourea moieties with different linkers were designed and synthesized. Some of the newly synthesized compounds were evaluated in vivo for their anti-hyperglycemic activities in STZ-induced hyperglycemic rats. Compounds 15_a, 15_e, 19_b and 24_a exhibited the highest anti-hyperglycemic activities with % reduction in blood glucose level of (50.58, 43.84, 45.10 and 49.62, respectively). Additionally, eight compounds revealed potent anti-hyperglycemic activities were further evaluated in vitro for their PPARγ binding affinity and insulin-secreting ability as potential mechanisms for anti-hyperglycemic activity. Four compounds (15_a, 15_b, 15_d and 15_e) significantly bound to PPARγ with IC₅₀ values of 0.482, 0.491, 0.350 and 0.369μM, respectively. Moreover, Compounds 15_a and 15_b have demonstrated induction of insulin-secretion with EC₅₀ values of 0.92 and 0.98μM, respectively. Furthermore, molecular docking and pharmacophore generation techniques were carried out to investigate binding patterns and fit values of the designed compounds with PPARγ and SUR, respectively.

Computational Methods Applied to Rational Drug Design

Due to the synergic relationship between medical chemistry, bioinformatics and molecular simulation, the development of new accurate computational tools for small molecules drug design has been rising over the last years. The main result is the increased number of publications where computational techniques such as molecular docking, de novo design as well as virtual screening have been used to estimate the binding mode, site and energy of novel small molecules. In this work I review some tools, which enable the study of biological systems at the atomistic level, providing relevant information and thereby, enhancing the process of rational drug design.

Modification of PBDEs (BDE-15, BDE-47, BDE-85 and BDE-126) biological toxicity, bio-concentration, persistence and atmospheric long-range transport potential based on the pharmacophore modeling assistant with the full factor experimental design

In this study, the properties of AhR binding affinity, bio-concentration factor, half-life and vapor pressure were selected as the typical indicators of biological toxicity, bio-concentration, persistence and atmospheric long-range transport potential for polybrominated diphenyl ethers (PBDEs), respectively. A three-dimensional pharmacophore modeling assistant with a full factor experimental design for each property was used to reveal the significant pharmacophore features and the substituent effects to obtain reasonable modified schemes for the selected target PBDEs. Finally, the performances of the persistent organic pollutant (POP) properties, the synthesis feasibility and the fire resistance of the modified compounds were evaluated. The most influential pharmacophore feature for all POP properties was the hydrophobic group, especially the vinyl and propyl groups. Modified compounds with two additional hydrophobic groups exhibited a better regulatory performance. The average reduction in the proportions of the four POP properties for the modified compounds (except for 3-phenyl-BDE-15) was 70.60%, 52.44%, 47.04% and 70.88%. In addition, the energy and the C-Br bond dissociation enthalpy of the four typical PBDEs were higher than those of the modified compounds (except for 3-phenyl-BDE-15), indicating the synthesis feasibility and the lower energy barrier of the modified compounds to release Br free radicals to provide fire resistance.

Identification of Structurally Diverse Antimicrobials Through Sequential Application of Pharmacophore Modeling, Virtual Screening, Molecular Docking and In Vitro Microbiological Assay

Dihydrofolate reductase enzyme has been an attractive biological target for the design and development of antimicrobials. Considering this, we have attempted to identify novel dihydrofolate reductase inhibitors through our well-defined in silico and in vitro work flow. An accurate and predictive pharmacophore model comprising of one hydrogen bond acceptor, two hydrophobic and one ring aromatic was developed and utilized as a query to search the National Cancer Institute and Maybridge database leading to retrieval of various compounds which were filtered on the basis of estimated activity, fit value and Lipinski's violation. Selected hits NSC3423, KM09759, NSC391, NSC2091 and HTS00630 were subjected to docking studies which resulted into visualization of potential interaction capabilities of hits in line to pharmacophoric features. The identified hits were evaluated for in vitro antimicrobial potential, and the results revealed that among all the five hits, NSC3423 is the most potent compound with activity against E. coli, P. aeruginosa, S. aureus, B. substilis, A. niger and F. oxysporum. On the other hand, KM09759, NSC391, NSC2091 and HTS00630 showed varying degree of activities against gram-positive, gram-negative and fungal strains.

In silico and in vitro screening to identify structurally diverse non-azole CYP51 inhibitors as potent antifungal agent

The problem of resistance to azole class of antifungals is a serious cause of concern to the medical fraternity and thus there is an urgent need to identify non-azole scaffolds with high affinity for lanosterol 14α-demethylase (CYP51). In view of this we have attempted to identify novel non-azole CYP51 inhibitors through the application of pharmacophore based virtual screening and in vitro evaluation. A rigorously validated pharmacophore model comprising of 2 hydrogen bond acceptor and 2 hydrophobic features has been developed and used to mine NCI database. Out of 265 retrieved hits, NSC 1215 and 1520 have been chosen on the basis of Lipinski's rule of five, fit and estimated values. Both the hits were docked into the active site of CYP51. In view of high fit value and CDocker score, NSC 1215 and 1520 have been subjected to in vitro microbiological assay. The result reveals that NSC 1215 and 1520 are active against Candida albicans, Candida parapsilosis, Candida tropicalis, and Aspergillus niger. In addition to this the absorption characteristics of both the hits have also been determined using the rat sac technique and permeation in order of NSC 1520>NSC 1215 has been observed.

Spectroscopic Study on the Interaction between Naphthalimide-Polyamine Conjugates and Bovine Serum Albumin (BSA)

The effect of a naphthalimide pharmacophore coupled with diverse substituents on the interaction between naphthalimide-polyamine conjugates 1–4 and bovine serum albumin (BSA) was studied by UV absorption, fluorescence and circular dichroism (CD) spectroscopy under physiological conditions (pH = 7.4). The observed spectral quenching of BSA by the compounds indicated that they could bind to BSA. Furthermore, caloric fluorescent tests revealed that the quenching mechanisms of compounds 1–3 were basically static type, but that of compound 4 was closer to a classical type. The K_sv values at room temperature for compound-BSA complexes-1-BSA, 2-BSA, 3-BSA and 4-BSA were 1.438 × 10⁴, 3.190 × 10⁴, 5.700 × 10⁴ and 4.745 × 10⁵, respectively, compared with the value of MINS, 2.863 × 10⁴ at Ex = 280 nm. The obtained quenching constant, binding constant and thermodynamic parameter suggested that the binding between compounds 1–4 with BSA protein, significantly affected by the substituted groups on the naphthalene backbone, was formed by hydrogen bonds, and other principle forces mainly consisting of charged and hydrophobic interactions. Based on results from the analysis of synchronous three-dimensional fluorescence and CD spectra, we can conclude that the interaction between compounds 1–4 and BSA protein has little impact on the BSA conformation. Calculated results obtained from in silico molecular simulation showed that compound 1 did not prefer either enzymatic drug sites I or II over the other. However, DSII in BSA was more beneficial than DSI for the binding between compounds 2–4 and BSA protein. The binding between compounds 1–3 and BSA was hydrophobic in nature, compared with the electrostatic interaction between compound 4 and BSA.

Target-based molecular modeling strategies for schistosomiasis drug discovery

Schistosomiasis, a neglected tropical disease caused by worms from the class Trematoda (genus Schistosoma), is a serious chronic condition that has been reported in approximately 80 countries. Nearly 250 million people are affected worldwide, mostly in the sub-Saharan Africa. Praziquantel, the mainstay of treatment, has been used for 30 years, and cases of resistance have been reported. The purpose of this perspective is to discuss current target-based molecular modeling strategies in schistosomiasis drug discovery. Advances in the field and the role played by the integration between computational modeling and experimental validation are also discussed. Finally, recent cases of the contribution of modern approaches in computational medicinal chemistry to the field are explored.

Exploring molecular fingerprints of selective PPARδ agonists through comparative and validated chemometric techniques

Peroxysome proliferator-activated receptors (PPARs) have grown greatly in importance due to their role in the metabolic profile. Among three subtypes (α, γ and δ), we here consider the least investigated δ subtype to explore the molecular fingerprints of selective PPARδ agonists. Validated QSAR models (regression based 2D-QSAR, HQSAR and KPLS) and molecular docking with dynamics analyses support the inference of classification-based Bayesian and recursive models. Chemometric studies indicate that the presence of ether linkages and heterocyclic rings has optimum influence in imparting selective bioactivity. Pharmacophore models and docking with molecular dynamics analyses postulate the occurrence of aromatic rings, HB acceptor and a hydrophobic region as crucial molecular fragments for development of PPARδ modulators. Multi-chemometric studies suggest the essential structural requirements of a molecule for imparting potent and selective PPARδ modulation.

Methods for generating and applying pharmacophore models as virtual screening filters and for bioactivity profiling

Biological effects of small molecules in an organism result from favorable interactions between the molecules and their target proteins. These interactions depend on chemical functionalities, bonds, and their 3D-orientations towards each other. These 3D-arrangements of chemical functionalities that make a small molecule active towards its target can be described by pharmacophore models. In these models, chemical functionalities are represented as so-called features. Commonly, they are obtained either from a set of active compounds or directly from the observed protein-ligand interactions as present in X-ray crystal structures, NMR structures, or docking poses. In this review, we explain the basics of pharmacophore modeling including dataset generation, 3D-representations and conformational analysis of small molecules, pharmacophore model construction, model validation, and its benefits to virtual screening and other applications.