Investigation of intermolecular interactions and binding mechanism of PU139 and PU141 molecules with p300 HAT enzyme via molecular docking, molecular dynamics simulations and binding free energy analysis.

The p300 histone acetyltransferase (HAT) enzyme acetylates the lysine residue of histone promotes the transcription reaction. The abnormal function of p300 HAT enzyme causes various diseases such as Cancer, Asthma, Alzheimer, Diabetics, and AIDS. In the recent years, several studies have been conducted to design potential drug to inhibit this enzyme. Recently, an in vitro study has been performed on the synthetic molecules PU139 and PU141 to inhibit the p300 HAT enzyme. The present study aims to understand the binding affinity, intermolecular interactions, conformational stability and binding energy of PU139 and PU141 molecules in the active site of p300 HAT enzyme from the in silico studies. The molecular docking and molecular dynamics (MD) simulations were carried out for both ligands with the p300 HAT enzyme. The molecular docking and MD simulations reveals that both molecules forms expected interactions with the catalytic site key residues of p300 enzyme. The MD simulation shows the maximum RMSD value for the PU141 is 2.3 Å, whereas for PU139 is 3.3 Å; these low RMSD values indicate that both molecules are highly stable in the active site of p300. The calculated binding free energy of PU141 (-20.62 kcal/mol) is higher than the molecule PU139 (-17.67 kcal/mol). Among the results, PU141 shows the high binding affinity with p300 while comparing with PU139. The results of this in-silico study coupled with the findings reported in the in vitro study confirm that PU141 may be suitable for clinical study.Communicated by Ramaswamy H. Sarma.

Halogen-Based 17ß-HSD1 Inhibitors: Insights from DFT, Docking, and Molecular Dynamics Simulation Studies.

The high expression of 17ß-hydroxysteroid dehydrogenase type 1 (17ß-HSD1) mRNA has been found in breast cancer tissues and endometriosis. The current research focuses on preparing a range of organic molecules as 17ß-HSD1 inhibitors. Among them, the derivatives of hydroxyphenyl naphthol steroidomimetics are reported as one of the potential groups of inhibitors for treating estrogen-dependent disorders. Looking at the recent trends in drug design, many halogen-based drugs have been approved by the FDA in the last few years. Here, we propose sixteen potential hydroxyphenyl naphthol steroidomimetics-based inhibitors through halogen substitution. Our Frontier Molecular Orbitals (FMO) analysis reveals that the halogen atom significantly lowers the Lowest Unoccupied Molecular Orbital (LUMO) level, and iodine shows an excellent capability to reduce the LUMO in particular. Tri-halogen substitution shows more chemical reactivity via a reduced HOMO-LUMO gap. Furthermore, the computed DFT descriptors highlight the structure-property relationship towards their binding ability to the 17ß-HSD1 protein. We analyze the nature of different noncovalent interactions between these molecules and the 17ß-HSD1 using molecular docking analysis. The halogen-derived molecules showed binding energy ranging from -10.26 to -11.94 kcal/mol. Furthermore, the molecular dynamics (MD) simulations show that the newly proposed compounds provide good stability with 17ß-HSD1. The information obtained from this investigation will advance our knowledge of the 17ß-HSD1 inhibitors and offer clues to developing new 17ß-HSD1 inhibitors for future applications.

Binding mechanism of spinosine and venenatine molecules with p300 HAT enzyme: Molecular screening, molecular dynamics and free-energy analysis.

The chromatin modification is regulated by the histone acetyltransferase (HAT) and histone deacetyltransferase (HDAC) enzymes; abnormal function of these enzymes leads to several malignant diseases. The inhibition of these enzymes using natural ligand molecules is an emerging technique to cure these diseases. The in vitro analysis of natural molecules, venenatine, spinosine, palmatine and taxodione are giving the best inhibition rate against p300 HAT enzyme. However, the detailed understanding of binding and the stability of these molecules with p300 HAT is not yet known. The aim of the present study is focused to determine the binding strength of the molecules from molecular dynamics simulation analysis. The docking analysis confirms that, the venenatine (-6.97 kcal/mol - conformer 8), spinosine (-6.52 kcal/mol conformer -10), palmatine (-5.72 kcal/mol conformer-3) and taxodione (-4.99 kcal/mol conformer-4) molecules form strong hydrogen bonding interactions with the key amino acid residues (Arg1410, Thr1411 and Trp1466) present in the active site of p300. In the molecular dynamics (MD) simulation, the spinosine retain these key interactions with the active site amino acid residues (Arg1410, Thr1411, and Trp1466) than venenatine and are stable throughout the simulation. The RMSD value of spinosine (0.5 to 1.3 Å) and venenatine (0.3 to 1.3 Å) are almost equal during the MD simulation. However, during the MD simulation, the intermolecular interaction between venenatine and the active site amino acid residues (Arg1410, Thr1411, and Trp1466) decreased on comparing with the spinosine-p300 interaction. The binding free energy of the spinosine (-15.30 kcal/mol) is relatively higher than the venenatine (-11.8 kcal/mol); this increment is attributed to the strong hydrogen bonding interactions of spinosine molecule with the active site amino acid residues of p300.

Investigation of binding mechanism and downregulation of elacestrant for wild and L536S mutant estrogen receptor-α through molecular dynamics simulation and binding free energy analysis.

The selective estrogen receptor downregulators (SERDs) are the new emerging class of drugs that are used for the treatment of endocrine resistance breast cancer. Elacestrant (ELA) is a new SERD, currently it is in phase II clinical trial. To understand the ELA-ERα interactions, the molecular docking analysis has been carried out. The ELA molecule binds with the helices H3, H5, H6, and H11 and forms important intermolecular interactions. In addition to this, the tetrahydronapthalene and phenyl rings of ELA are forming T-shaped π···π interactions with the Phe404 and Trp383 residues. Further to understand the stability and flexibility of ELA molecule in the active site of wild and mutated L536S ERα, 100ns molecular dynamics (MD) simulation was performed for both complexes. Interestingly, the MD analysis of wild complex revealed an interaction between ELA and the Asn532 of H11, which is an essential interaction for the downregulation/degradation of ERα, whereas this interaction is not observed in the mutated complex. The drug binding mechanism and H12 dynamics have been elucidated from the analysis of hydrogen bonding interactions and the secondary structure analysis. To explore the binding affinity of ELA molecule, the binding free energy and normal mode analyses were carried out. The per residue decomposition analysis also performed, which shows the contribution of individual amino acids. The principal component analysis and residue interaction network analysis were used to identify the modifications and the interaction between the residues. From the results of different analysis, the inhibition mechanism and downregulation of ERα-ELA complex has been investigated. © 2019 Wiley Periodicals, Inc.

Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations.

The resistance to the endocrine therapy of breast cancer leads to the emergence of new class of drugs that downregulates the estrogen receptor action known as selective estrogen receptor downregulators (SERDs). The first approved SERD is fluvestrant; after this, there are several downregulators evolved and are in clinical trials, in which the brilanestrant (BRI) molecule shows nM range of binding affinity and efficacy. In the present study, to understand the binding nature of BRI molecule in the active site of ERα, the molecular docking analysis has been performed. Further, the QM/MM calculations were performed for the BRI-ERα complex to analyze the charge density distribution of intermolecular interactions. The molecular dynamics (MD) simulation was employed to understand the stability and binding mechanism of BRI molecule through root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF) and binding free energy calculations. From the MD simulation trajectory analysis, the alterations of Helix12 conformation and the key residue (Lys529), which is responsible for the ERα downregulation, have been identified. Further, the interaction between the H3 and H12 regions was identified for the antagonism of BRI molecule. The current study led us to understand the binding mechanism, antagonism and downregulation of BRI molecule, and this knowledge is essential to design novel SERDs for the treatment of endocrine-resistant positive breast cancer.Communicated by Ramaswamy H. Sarma.

In vitro and in silico analysis of novel astaxanthin-s-allyl cysteine as an inhibitor of butyrylcholinesterase and various globular forms of acetylcholinesterases.

In Alzheimer's disease (AD) and diabetes-associated cognitive decline, the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activity is increased. AChE exists as different globular molecular forms: tetramer (G4), dimer (G2) and monomer (G1). In adult brain, G4 form is abundant however in AD, the ratio of lower molecular forms (G1) to G4 form increased. Hence, the present study delineated the inhibition of novel astaxanthin-s-allyl cysteine (AST-SAC) against BChE and various molecular forms of AChE. Cobra venom, human erythrocyte and Electrophorus electricus was used as source of G1, G2 and G4 form of AChE. AST-SAC showed inhibition against G1 (IC50 = 0.72 µM, competitive, Ki = 0.66 µM), G2 (IC50 = 0.65 µM, mixed, Ki = 0.50 µM) and G4 (IC50 = 0.67 µM, competitive, Ki = 0.67 µM) form of AChE. AST-SAC inhibited human brain AChE (IC50 = 0.84 µM, competitive, Ki = 0.53 µM) and human serum BChE (IC50 = 0.80 µM, competitive, Ki = 0.58 µM). In silico analysis revealed the interaction of AST-SAC with the amino acids present in peripheral anionic and catalytic site of human AChE and BChE. Molecular dynamics simulation confirmed the stable interaction of AST-SAC in the active site gorge of AChE and BChE.

S-allyl cysteine as potent anti-gout drug: Insight into the xanthine oxidase inhibition and anti-inflammatory activity.

S-allyl cysteine (SAC) is known for its various beneficial effects such as neuroprotection and immunomodulation. The beneficial effect of SAC against gout has not been explored. The present study aims to describe the two roles of SAC: (1) inhibitory effect against xanthine oxidase (XO) enzyme activity; and (2) anti-inflammatory property against MSU crystal-induced gouty inflammation in rat. The inhibitory effect of SAC against bovine XO enzyme activity was determined in vitro. In silico analysis was carried out to determine the intermolecular interaction between SAC and bovine XO. MSU crystal was injected in the right paw of the rat to induce gouty inflammation. SAC (40 mg/kg body weight) and colchicine (positive control; 1 mg/kg body weight) was given for 3 days. At the end of the treatment, the oxidative stress, antioxidant parameters and mitochondrial function were determined in the ankle joint tissue. The concentration of inflammatory cytokines such as TNF-α and IL-1ß was measured in the serum using ELISA. SAC inhibited (IC50 value, 33 µg/ml) XO enzyme activity in a competitive mode with corresponding Ki value of 4 µg/ml. In silico analysis predicted the interaction of SAC with the amino acids such as Arg880, Phe798, Phe914 and Phe1009 of XO enzyme. The root mean square deviation, root mean square fluctuation and free energy calculation values confirmed the stable SAC-XO interaction. The inhibition of SAC on XO enzyme activity in in vivo was further confirmed by silkworm model. SAC through reducing oxidative stress, enhancing antioxidants, protecting mitochondrial function has shown anti-inflammatory effect against MSU crystal-induced gout which was observed as reduced level of inflammatory markers in the serum. The medicinal potential of SAC as a preventive agent through its XO inhibitory property as well as curative agent through its anti-inflammatory property against gout has been understood from the present study.

Biological interaction of newly synthesized astaxanthin-s-allyl cysteine biconjugate with Saccharomyces cerevisiae and mammalian α-glucosidase: In vitro kinetics and in silico docking analysis.

In humans, alpha-glucosidase activity is present in sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM). α-glucosidase is involved in the hydrolyses of disaccharide into monosaccharides and results in hyperglycemia. Subsequently chronic hyperglycemia induces oxidative stress and ultimately leads to the secondary complications of diabetes. Hence, identifying compounds with dual beneficial activity such as efficient antioxidant and α-glucosidase inhibition property has attracted the attention in recent years. Keeping these views, in the present study astaxanthin (AST; a natural antioxidant present in marine microalgae) was biconjugated with allyl sulfur amino acid such as s-allyl cysteine (SAC). The synthesized AST-SAC (with molecular weight of 883.28) was characterized using UV-visible spectrophotometer, ESI-MS, and NMR analysis. AST-SAC showed potent antioxidant property in vitro. AST-SAC inhibited Saccharomyces cerevisiae α-glucosidase (IC50 = 3.98 µM; Ki = 1 µM) and mammalian α-glucosidase [rat intestinal maltase (IC50 = 6.4 µM; Ki = 1.3 µM) and sucrase (IC50 = 1.6 µM; Ki = 0.18 µM)] enzyme activity in a dose-dependent manner. Kinetic analysis revealed that AST-SAC inhibited all the α-glucosidases in a competitive mode. In silico analysis determined the interaction of AST-SAC with the amino acids present in the active site of S. cerevisiae and human (MGAM and SI) α-glucosidases.

S-allyl-glutathione, a synthetic analogue of glutathione protected liver against carbon tetrachloride toxicity: Focus towards anti-oxidative efficiency.

A simple analogue of well known natural antioxidant glutathione (GSH) called S-allyl-glutathione (SAG) was evaluated against carbon tetrachloride (CCl4)-induced oxidative stress liver injury in rat. Pretreatment of SAG attenuated the CCl4-toxicity induced elevation of liver injury markers such as enzymes (AST, ALT, GGT, ALP and LDH) and bilirubin in the blood circulation. Such protective effect of SAG resulted in preservation of liver function observed as normal level of total protein and albumin in plasma as well as inhibition of dyslipidemia in liver. In addition, in silico analysis has proved that SAG has strong affinity with the amino acids present in active site of the human cytochrome P450 2E1 and 3A4. Three important mechanisms provided by SAG such as scavenging of reactive oxidants, replenishing of endogenous antioxidants (SOD, catalase, GPx, GSH and vitamin C) and protection of mitochondrial function (oxidative phosphorylation complex activities) are involved in the optimal function of liver against CCl4-toxicity.