Comparative Study of Binding Pockets in Human CYP1A2, CYP3A4, CYP3A5, and CYP3A7 with Aflatoxin B1, a Hepato-Carcinogen, by Molecular Dynamics Simulation & Principal Component Analysis.

BACKGROUND: Aflatoxin B1 is a harmful hepatocarcinogen which is metabolized in our body by Cytochrome P450 enzymes, namely CYP1A2, CYP3A4, CYP3A5, and CYP3A7, into toxic (exo-8, 9-epoxide) and nontoxic (AFQ1, endo-epoxide) products. We have found from the literature that due to cooperativity, the rate of metabolic reactions increases in CYP1A2 and CYP3A4 involving more than one site of proteins to form two products at a given time, whereas the interaction of CYP3A5 and CYP3A7 is still unknown. Our work aims to study these four enzymes with AFB1 based on binding site pocket characterization and to find the probable resultant products at each binding site. METHODS: We used computational approaches like homology modeling, molecular docking to form mono and double ligated systems, molecular dynamic simulations to analyze the potential energies (vdW & electrostatic), PCA, RMSF, and residue-wise interactions at the active as well as allosteric sites of these four enzymes. RESULTS: We found that CYP1A2, CYP3A4, and CYP3A5 were more hydrophobic at the first site and may induce epoxidation reaction to form toxic products, whereas the second site would be expected to be more polar and comprising charged interactions, thus enhancing non-toxic hydroxylated products. However, in CYP3A7, the first site favors hydroxylation, whereas the second site is involved in higher hydrophobic interactions. CONCLUSION: Thus, in the fetus where AFB1 is metabolized only by CYP3A7, a lower concentration of toxic metabolites will be expected, while in adults exhibiting CYP1A2, CYP3A4 and CYP3A5 may increase the concentration of the toxic metabolites due to the combined effect of these enzymes, consequently increasing liver toxicity. We believe that AFB1 binding characteristics will be helpful for medicinal chemists in the process of designing a new drug.

Identification of a less toxic vinca alkaloid derivative for use as a chemotherapeutic agent, based on in silico structural insights and metabolic interactions with CYP3A4 and CYP3A5.

Vinca alkaloids are chemotherapeutic agents used in the treatment of both pediatric and adult cancer patients. Cytochrome P450 3A5 (CYP3A5) is 9- to 14-fold more efficient at clearing vincristine than cytochrome P450 3A4 (CYP3A4) is. However, patients who express an inactive form of the polymorphic CYP3A5 enzyme suffer from severe neurotoxicity during vincristine treatment, resulting in chemotherapy failure. Previous studies have found that the addition of new features to the parent drug can enhance its binding affinity to tubulin manyfold and could therefore yield novel anticancer drugs. However, there is no report of any study of the metabolic activities of CYP3A4 and CYP3A5 with respect to vincristine and vinblastine, so we studied the interactions of these two drugs and 15 vinca derivatives with CYP3A4 and CYP3A5 by performing docking studies using GOLD. Six of the vinca derivatives in complexes with CYP3A4 and CYP3A5 were further investigated in 100-ns molecular dynamic simulations. Interaction energies, hydrogen bonds, and linear interaction energies were calculated and principal component analysis was carried out to visualize the binding interface in each complex. The results indicate that the addition of dimethylurea at the C20' position in vincristine may increase its binding affinity and lead to enhanced interactions with the less polymorphic CYP3A4 rather than CYP3A5. Thus, dimethylurea vincristine may be a useful drug in cancer chemotherapy treatment as it should be significantly less likely than vincristine to induce severe neurotoxicity in patients. Graphical Abstract Proposed modification of Vinca alkaloid derivatives to decrease the neurotoxicity level in cancer patients exhibiting CYP3A4 gene rather than polymorphic CYP3A5 gene.

Differential Interactions of Cytochrome P450 3A5 and 3A4 with Chemotherapeutic Agent-Vincristine: A Comparative Molecular Dynamics Study.

The chemotherapeutic agent vincristine, used for treatment of acute lymphoblastic leukemia is metabolized preferentially by polymorphic cytochrome P450 3A5 (CYP3A5) with higher clearance rate than cytochrome P450 3A4 (CYP3A4). As a result, CYP3A5 expressers have a reduced amount of vincristine-induced peripheral neuropathy than non-expressers. We modeled the structure of CYP3A5 and its interaction with vincristine, compared with CYP3A4-vincristine complex using molecular docking and simulation studies. This relative study helped us to understand the molecular mechanisms behind the interaction at the atomic level through interaction energy, binding free energy, hydrogen bond and solvent accessible surface area analysis - giving an insight into the binding mode and the main residues involved in this particular interaction. Our results show that the interacting groups get closer in CYP3A5-vincristine complex due to different orientation of vincristine. This leads to higher binding affinity of vincristine towards CYP3A5 compared to CYP3A4 and explains the preferential metabolism of vincristine by CYP3A5. We believe that, the results of the current study will be helpful for future studies on structure-based drug design in this area.

Meliloester, a new melilotic ester from Melilotus alba.

A new melilotic ester, meliloester [2-ethyl-hexyl-3-(2-hydroxyphenyl) propionate], was isolated from the whole plant of Melilotus alba. Its structure was elucidated on the basis of spectroscopic and mass spectrometric analyses, including EI-MS, HR-MS, and UV, IR, 1D and 2D-NMR spectroscopic studies.

A new eudesmane sesquiterpene from Pluchea arguta.

A new eudesmane sesquiterpene, pluchargen A (3-beta-[3'-chloro-2'-hydroxy-2'-methyl butyroyl]-cuauhtemone), was isolated from the whole plant of Pluchea arguta, and the structure was elucidated on the basis of 1- and 2-D NMR spectroscopic studies.

Separation and identification of a new saponin from the flowers of Guaiacum officinale L.

A triterpenoid saponin, guaianin O (1), oleanolic acid 3-O-{α-L-rhamnopyranosyl-(1 → 2)-[ß-D-glucopyranosyl-(1 → 3)]-α-L-arabinopyranoside}-28- O-[ß-D-glucopyranosyl]-ester, was isolated from the n-butanol extract of flowers of Guaiacum officinale L. The structural elucidation of 1 was accomplished by extensive studies of both one and two dimensional ¹H, ¹³C-NMR spectra, the FAB mass spectrum, and alkaline and acid hydrolyses.

Triterpenoid saponin from the bark of Guaiacum officinale L.

A new triterpenoid saponin, guaianin R (1) was isolated from the n-BuOH extract of bark of Guaiacum officinale L. It was characterized as akebonic acid-3-O-[alpha-L-rhamnopyranosyl-(1 --> 3)-beta-D-glucopyranosyl-(1 --> 3)-alpha-L-rhamnopyranosyl-(1 --> 2)-alpha-L-arabinopyranoside]-28-O-[beta-D-glucopyranosyl]-ester. The structure was established with the help of a comparative study of 1D and 2D 1H- 13C NMR methods. A number of other saponins were isolated and reported from the same species.

Isolation and structure elucidation of three glycosides and a long chain alcohol from Polianthes tuberosa Linn.

Three glycosides and a long chain alcohol were isolated from the bulbs of Polianthes tuberosa, these were identified as 3,29-dihydroxystigmast-5-ene-3-O-beta-D-galactopyranoside (1), ethyl beta-D-galactopyranoside (2), ethyl-alpha-D-galactopyranoside (3), and 1-tricosanol (4). The structures were determined by extensive spectroscopic and chemical methods. All four isolated compounds were screened for their cytotoxicity, antibacterial and antifungal activities, none of the compounds showed any significant activity.