A Study on Docking Mode of HIV Protease and Their Inhibitors

Aedes aegypti juvenile hormone acid methyl transferase, the ultimate enzyme in the biosynthetic pathway of juvenile hormone III, exhibits substrate control

We report on the cloning, sequencing, characterization, 3D modeling and docking of Aedes aegypti juvenile hormone acid methyl transferase (AeaJHAMT), the enzyme that converts juvenile hormone acid (JHA) into juvenile hormone (JH). Purified recombinant AeaJHAMT was extensively characterized for enzymatic activity and the Michaelis Menten kinetic parameters Km, Vmax, k(cat) (turn over number) and k(cat)/Km (catalytic efficiency) using JHA and its analogues as substrates. AeaJHAMT methylates JHA III 5-fold faster than farnesoic acid (FA). Significant differences in lower methyl transferase (MT) activities towards the cis/trans/trans, cis/trans/cis and the trans/cis/cis isomers of JHA I (1.32, 4.71 and 156-fold, respectively) indicate that substrate chirality is important for proper alignment at the catalytic cavity and for efficient methyl transfer by S-adenosyl methionine (SAM). Our 3D model shows a potential binding site below the main catalytic cavity for JHA analogues causing conformational change and steric hindrance in the transfer of the methyl group to JHA III. These, in silico, observations were corroborated by, in vitro, studies showing that several JHA analogues are potent inhibitors of AeaJHAMT. In vitro, and in vivo studies using [(3)H-methyl]SAM show that the enzyme is present and active throughout the adult life stage of A. aegypti. Tissue specific expressions of the JHAMT gene of A. aegypti (jmtA) transcript during the life cycle of A. aegypti show that AeaJHAMT is a constitutive enzyme and jmtA transcript is expressed in the corpora allata (CA), and the ovary before and after the blood meal. These results indicate that JH III can be synthesized from JHA III by the mosquito ovary, suggesting that ovarian JH III may play an important physiological role in ovarian development and reproduction. Incubating AeaJHAMT with highly pure synthetic substrates indicates that JHA III is the enzyme's preferred substrate, suggesting that AeaJHAMT is the ultimate enzyme in the biosynthetic pathway of JH III.

Interaction of fullerenol with lysozyme investigated by experimental and computational approaches

The potential biomedical applications of fullerenol C(60)(OH)(x) (x≈24) have been extensively studied. However, the structural information of the interaction of fullerenol with the bio-system at the molecular level, which is essential for understanding its bioactivity and toxicity, is still missing. In this study, lysozyme was selected as a model protein to investigate the interaction between fullerenol and biomolecules. A strong induced circular dichroism (CD) signal of achiral fullerenol was observed after binding with lysozyme. Activity assay shows that lysozyme activity is inhibited significantly by fullerenol. No heat capacity difference between the folded and unfolded states of lysozyme was measured by differential scanning calorimetry (DSC) in the presence of fullerenol, indicating that fullerenol prefers to bind with the hydrophobic residues. Both experimental and Autodock computational results suggest that the binding site on lysozyme for fullerenol is close to Trp 62, and a π-π stacking interaction might play an important role in binding.

Design of ligand binding to an engineered protein cavity using virtual screening and thermal up-shift evaluation

Proteins could be used to carry and deliver small compounds. As a tool for designing ligand binding sites in protein cores, a three-step virtual screening method is presented that has been optimised using existing data on T4 lysozyme complexes and tested in a newly engineered cavity in flavodoxin. The method can pinpoint, in large databases, ligands of specific protein cavities. In the first step, physico-chemical filters are used to screen the library and discard a majority of compounds. In the second step, a flexible, fast docking procedure is used to score and select a smaller number of compounds as potential binders. In the third step, a finer method is used to dock promising molecules of the hit list into the protein cavity, and an optimised free energy function allows discarding the few false positives by calculating the affinity of the modelled complexes. To demonstrate the portability of the method, several cavities have been designed and engineered in the flavodoxin from Anabaena PCC 7119, and the W66F/L44A double mutant has been selected as a suitable host protein. The NCI database has then been screened for potential binders, and the binding to the engineered cavity of five promising compounds and three tentative non-binders has been experimentally tested by thermal up-shift assays and spectroscopic titrations. The five tentative binders (some apolar and some polar), unlike the three tentative non-binders, are shown to bind to the host mutant and, importantly, not to bind to the wild type protein. The three-step virtual screening method developed can thus be used to identify ligands of buried protein cavities. We anticipate that the method could also be used, in a reverse manner, to identify natural or engineerable protein cavities for the hosting of ligands of interest.

Taxane analogues against breast cancer: a quantitative structure-activity relationship study

Breast cancer is the second leading cause of cancer death among women in the United States. Two taxane analogues, taxol and taxotere, are the most important antimitotic drugs currently in clinical use for the treatment of breast cancers. However, recent reports have indicated that the use of these drugs often results in various undesired side effects as well as multi-drug resistance. These limitations have led to the development of new taxane derivatives with fewer side effects, superior pharmacological properties, and improved anticancer activity to maximize the induced benefits for breast cancer patients. Herein, four series of taxane derivatives were used to correlate their inhibitory activities against breast cancer cells with their hydrophobic and steric properties in order to understand their chemical-biological interactions. The resulting QSARs show that the inhibitory activities of taxane analogues against breast cancers are mainly dependent either on their hydrophobicity or the hydrophobic/molar refractivity descriptor of their substituents. A parabolic correlation with MR(Y) is the most encouraging example, in which the optimum value of this parameter is well defined. We believe this correlation may prove to be an adequate predictive model that can help provide guidance in design and synthesis and subsequently yield highly specific compounds that may have high anti-breast-cancer activity with fewer side effects and superior pharmacological properties. On the basis of this QSAR model, five compounds are suggested as potential synthetic targets. Internal (cross-validation (LOO-q(2) and LMO-q(2)), quality factor (Q), Fischer statistics (F), and Y-randomization) and external validation tests have validated all the QSAR models.

Complement C1q-target proteins recognition is inhibited by electric moment effectors

Classical complement pathway is an important innate immune mechanism, which is usually triggered by binding of C1q to immunoglobulins, pentraxins and other target molecules. Although the activation of the classical pathway is crucial in the host defence, its undesirable and uncontrolled activation can lead to tissue damage. Thus, understanding the molecular basis of complement activation and its inhibition are of great biomedical importance. Recently, we proposed a mechanism for target recognition and classical pathway activation by C1q, which is likely governed by calcium-controlled reorientation of macromolecular electric moment vectors. Here we sought to define the mechanism of C1q inhibition by low molecular weight disulphate compounds that bind to the globular (gC1q) domain, using experimental, computational docking and theoretical modelling approaches. Our experimental results demonstrate that betulin disulphate (B2S) and 9,9-bis(4'-hydroxyphenyl)fluorene disulphate (F2S) inhibit the interaction of C1q and its recombinant globular modules with target molecules IgG1, C-reactive protein (CRP) and long pentraxin 3 (PTX3). In most C1q-inhibitor docked complexes, there is a reduction of electric moment scalar values and similarly altered direction of electric/dipole moment vectors. This could explain the inhibitory effect by impaired electrostatic steering, lacking optimal target recognition and formation of functional complex. In the presence of the inhibitor, the tilt of gC1q domains is likely to be blocked by the altered direction of the electric moment vector. Thus, the transition from the inactive (closed) towards the active (open) conformation of C1q (i.e. the complement activation signal transmission) will be impaired and the cascade initiation disrupted. These results could serve as a starting point for the exploration of a new form of 'electric moment inhibitors/effectors'.

Antitumor studies -- part 2: structure-activity relationship study for flavin analogs including investigations on their in vitro antitumor assay and docking simulation into protein tyrosine kinase

Various analogs of flavins, 5-deazaflavins, and flavin-5-oxides were docked into the binding site of protein tyrosine kinase pp60(c-src), and some of them were assayed for their potential antitumor and PKC (protein kinase C) inhibitory activities in vitro. The results considering SAR (structure-activity relationship) revealed that the higher binding affinities obtained include compounds with the structure modifications on the flavin or 5-deazaflavin skeleton, namely, NH(2) or Ph (phenyl-) group at the C-2 position and so on. Computationally designed compounds 4a, 6a, b, 7, 11b, c, 12, 15, and 22c exhibited good docking results suggesting that they are potentially active antitumor agents. These compounds have 1-3 phenyl moieties, which are thought to be responsible for the planar aromatic fitting or electrostatic attraction onto the groove of the binding pocket.