Evaluation of Phytopolyphenols for their gp120-CD4 Binding Inhibitory Properties by In Silico Molecular Modelling & In Vitro Cell Line Studies.

BACKGROUND: Lack of effective early-stage HIV-1 inhibitor instigated the need for screening of novel gp120-CD4 binding inhibitor. Polyphenols, a secondary metabolite derived from natural sources are reported to have broad spectrum HIV-1 inhibitory activity. However, the gp120-CD4 binding inhibitory activity of polyphenols has not been analysed in silico yet. OBJECTIVES: To establish the usage of phytopolyphenols (Theaflavin, Epigallocatechin (EGCG), Ellagic acid and Gallic acid) as early stage HIV-1 inhibitor by investigating their binding mode in reported homology of gp120-CD4 receptor complex using in silico screening studies and in vitro cell line studies. METHODS: The in silico molecular docking and molecular simulation studies were performed using Schrödinger 2013-2 suite installed on Fujitsu Celsius Workstation. The in vitro cell line studies were performed in the TZM-bl cell line using MTT assay and ß-galactosidase assay. RESULTS: The results of molecular docking indicated that Theaflavin and EGCG exhibited high XP dock score with binding pose exhibiting Van der Waals interaction and hydrophobic interaction at the deeper site in the Phe43 cavity with Asp368 and Trp427. Both Theaflavin and EGCG form a stable complex with the prepared HIV-1 receptor and their binding mode interaction is within the vicinity 4 Å. Further, in vitro cell line studies also confirmed that Theaflavin (SI = 252) and EGCG (SI = 138) exert better HIV-1 inhibitory activity as compared to Ellagic acid (SI = 30) and Gallic acid (SI = 34). CONCLUSION: The results elucidate a possible binding mode of phytopolyphenols, which pinpoints their plausible mechanism and directs their usage as early stage HIV-1 inhibitor.

Tetrahydrocurcumin-loaded vaginal nanomicrobicide for prophylaxis of HIV/AIDS: in silico study, formulation development, and in vitro evaluation.

A vaginal microbicide is a front-line women-dependent approach and an alternative to a condom for prevention of unprotected sexual intercourse-associated HIV. The microbicide research is still in its infancy with several products in the clinical studies being reported to have good efficacy, safe, but with poor adherence. One such molecule reported with an excellent efficacy when tested preclinically is curcumin, a natural polyphenol derived from Curcuma longa. Despite its potential HIV-1 inhibitory activity, it has intense yellow color staining properties, which would result in poor consumer compliance and adherence for vaginal application. To address this issue, tetrahydrocurcumin (THC), a colorless derivative of curcumin, was subjected to in silico screening (molecular docking and dynamics simulation studies) using homology model of gp120-CD4 binding. It was found that THC exhibited equivalent gp120-CD4 binding inhibitory activity as compared with curcumin due to its stable hydrophobic interactions with residues Asp368 and Trp427 deeper in the Phe43 cavity of CD4 receptor. Hence, it can be effectively used as a potential microbicide candidate. THC, a BCS Class II molecule exhibits poor solubility, spreadability, and intracellular uptake when used in the conventional form. Thus, it was decided to develop a lipid-based nanomicrobicide gel for delivery of THC. The developed THC-loaded o/w microemulsion gel was characterized for physicochemical properties (globule size, drug content, drug release, and permeation) and further used for in vitro cell line studies (cell viability, cellular uptake, and anti-HIV activity). The developed formulation was found to be stable with coitus-independent release profile and exhibited a rapid time-independent intracellular uptake. In addition, it exhibited a fourfold increase in efficacy as compared with conventional THC. Thus, the novel THC-loaded o/w microemulsion gel exhibited the potential for prevention of HIV-1 infection associated with unprotected sexual intercourse.

Design and synthesis of 5-(5-nitrothiophen-2-yl)-3-phenyl-4,5-dihydro-1H-pyrazole derivatives with improved solubility and potential antituberculosis activity.

We report the design-synthesis of several nitrothiophene containing molecules as antituberculosis agents. The molecules were designed on the basis of previously reported nitrofuran molecules in our laboratory, and the α,ß-unsaturated linker was modified to cyclized linker in order to overcome the challenge of low solubility and possible toxicity. The stereo-electronic properties such as HOMO, LUMO, and HOMO-LUMO gap along with other properties such as aqueous solvation energies and QPLogS values were studied. The designed molecules were synthesized and tested for in vitro antituberculosis activity, and some molecules were found to be highly active comparable to standard drugs. Further, the aqueous solubility was determined using visual inspection method and the designed molecules were found to be more soluble than their chalcone counterparts. Cytotoxicity studies were performed and the molecules were found to be non-cytotoxic. Electroanalytical studies proved nitro reduction as the mechanism of action for these molecules. Thus, this study provides potential nitrothiophene containing hits with improved solubility and reduced chances of toxicity.

Molecular dynamic simulations on an inhibitor of anti-apoptotic Bcl-2 proteins for insights into its interaction mechanism for anti-cancer activity.

Inhibition of normal cellular apoptosis or programed cell death is the hallmark of all cancers. Apoptotic dysregulation can result in numerous pathological conditions, such as cancers, autoimmune disorders, and neurodegeneration. Members of the BCL-2 family of proteins regulate the process of apoptosis by its promotion or inhibition and overexpression of the pro-survival anti-apoptotic proteins (Bcl-2, Bcl-xL, and Mcl-1) has been associated with tumor maintenance, growth and progression Small molecules and peptides which bind the BH3 binding groove of these proteins have been explored in the recent times for their anticancer potential. The first anticancer agents targeting this family of proteins were aimed primarily toward inhibition of Bcl-2. An elevated level of Mcl-1, despite Bcl-2 inhibition, continues to be a cause for resistance in most cancers. However, in silico exploration of Mcl-1 specific drugs and their associated mechanisms have not been clearly elucidated. In order to understand the same, we have carried out docking and molecular dynamic simulations on ABT-263 (Navitoclax), an orally active inhibitor of Bcl-2, Bcl-xL, and Bcl-w proteins; Obatoclax, a pan-Bcl-2 inhibitor as well as Maritoclax, an Mcl-1 specific inhibitor. Docking studies revealed that binding to the hydrophobic grooves is a prerequisite for action on the BCL protein and the binding mechanism and chemical space utilization dictates stability as well as specificity of the inhibitor molecular dynamic simulations showed that on binding, the α-helices of these proteins exhibited less fluctuations than loop regions, also hydrophobic contacts and hydrogen bonding were observed to be the predominant interactions in the drug-receptor complexes. Communicated by Ramaswamy H. Sarma.

Homology modelling of human divalent metal transporter (DMT): Molecular docking and dynamic simulations for duodenal iron transport.

Iron transport through the duodenum is regulated by carrier proteins, one of which is the ubiquitously distributed divalent metal transporter (DMT1) which is responsible for the uptake of iron across the apical surface of the duodenal enterocyte. The crystallographic structure of Staphylococcus capitis divalent metal ion transporter (ScaDMT1) was obtained and it was used as a template for the construction of a homology model of human divalent metal transporter (hDMT1). The binding site for hDMT1 was determined by using SiteMap as well as molecular docking studies on ScaDMT1. The differences in binding modes between ScaDMT1 and hDMT1 were noted for a set of 7 iron containing compounds, including ferrous sulphate. Diffusion of ferrous ion was observed during the course of molecular dynamic simulation which corresponded to the postulated mechanism of iron transport. Further, the dock scores correlated well with relative bioavailabilities of the iron compounds. The study confirmed the efficacy of the in silico model which could be used for future studies on the absorption of micronutrients.

Insights into the Interaction Mechanism of Ligands with Aß42 Based on Molecular Dynamics Simulations and Mechanics: Implications of Role of Common Binding Site in Drug Design for Alzheimer's Disease.

Aggregation of ß-amyloid (Aß) into oligomers and further into fibrils is hypothesized to be a key factor in pathology of Alzheimer's disease (AD). In this study, mapping and docking were used to study the binding of ligands to protofibrils. It was followed by molecular simulations to understand the differences in interactions of known therapeutic agents such as curcumin, fluorescence-based amyloid staining agents such as thioflavin T, and diagnostic agents such as florbetapir (AV45), with Aß protofibrils. We show that therapeutic agents bind to and distort the protofibrils, thus causing destabilization or prevention of oligomerization, in contrast to diagnostic agents which bind to but do not distort such structures. This has implications in the rational design of ligands, both for diagnostics and therapeutics of AD.

Pharmacophore based 3DQSAR of phenothiazines as specific human butyrylcholinesterase inhibitors for treatment of Alzheimer's disease.

Quantitative three dimensional structure activity relationship (3D-QSAR) studies were performed on phenothiazine derivatives as Butyrylcholinesterase (BuChE) inhibitors. Pharmacophore Alignment and Scoring Engine (PHASE) was used to develop predictive Common Pharmacophore Hypotheses (CPHs). The alignment thus obtained was used for Comparative Molecular Field Analysis (CoMFA)/Comparative Molecular Similarity Indices Analysis (CoMSIA) model development. A fourpoint common pharmacophore hypothesis, comprising of one acceptor, one hydrophobic region and two aromatic ring centres was generated. A structurally diverse set of 80 molecules was used of which 56 were grouped into training set to develop the model and the rest 24 molecules into test set to validate the CoMFA/CoMSIA models. The models so developed showed a good r(2)predictive of 0.7587 for CoMFA and 0.7737 for CoMSIA. CoMFA and CoMSIA models had excellent Q(2) (cross-validated coefficient) of 0.7125 and 0.7093, respectively which showed high correlative and predictive abilities of the models. The 3-D contour maps of CoMFA/CoMSIA provided interpretable explanation of SAR for the compounds and also permitted interesting conclusions about the substituent effects on the phenothiazine derivatives. The outcomes of the study would help in the rational design of novel and potent therapeutic agents as specific BuChE inhibitors for symptomatic or disease modifying treatment of AD.