J. Muthukumaran

ZifBASE: a database of zinc finger proteins and associated resources

BackgroundInformation on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develop chimeric proteins for targeted genome engineering and site-specific gene correction. There is a need to develop a computational resource of zinc finger proteins (ZFP) to identify the potential binding sites and its location, which reduce the time of in vivo task, and overcome the difficulties in selecting the specific type of zinc finger protein and the target site in the DNA sequence.DescriptionZifBASE provides an extensive collection of various natural and engineered ZFP. It uses standard names and a genetic and structural classification scheme to present data retrieved from UniProtKB, GenBank, Protein Data Bank, ModBase, Protein Model Portal and the literature. It also incorporates specialized features of ZFP including finger sequences and positions, number of fingers, physiochemical properties, classes, framework, PubMed citations with links to experimental structures (PDB, if available) and modeled structures of natural zinc finger proteins. ZifBASE provides information on zinc finger proteins (both natural and engineered ones), the number of finger units in each of the zinc finger proteins (with multiple fingers), the synergy between the adjacent fingers and their positions. Additionally, it gives the individual finger sequence and their target DNA site to which it binds for better and clear understanding on the interactions of adjacent fingers. The current version of ZifBASE contains 139 entries of which 89 are engineered ZFPs, containing 3-7F totaling to 296 fingers. There are 50 natural zinc finger protein entries ranging from 2-13F, totaling to 307 fingers. It has sequences and structures from literature, Protein Data Bank, ModBase and Protein Model Portal. The interface is cross linked to other public databases like UniprotKB, PDB, ModBase and Protein Model Portal and PubMed for making it more informative.ConclusionA database is established to maintain the information of the sequence features, including the class, framework, number of fingers, residues, position, recognition site and physio-chemical properties (molecular weight, isoelectric point) of both natural and engineered zinc finger proteins and dissociation constant of few. ZifBASE can provide more effective and efficient way of accessing the zinc finger protein sequences and their target binding sites with the links to their three-dimensional structures. All the data and functions are available at the advanced web-based search interface http://web.iitd.ac.in/~sundar/zifbase.

Analysis of CYP3A4-HIV-1 protease drugs interactions by computational methods for Highly Active Antiretroviral Therapy in HIV/AIDS

HIV infected patients often take at least three anti-HIV drugs together in Highly Active Antiretroviral Therapy (HAART) and/or Ritonavir-Boosted Protease Inhibitor Therapy (PI/r) to suppress the viral replications. The potential drug-drug interactions affect efficacy of anti-HIV treatment and major source of such interaction is competition for the drug metabolizing enzyme, cytochrome P450 (CYP). CYP3A4 isoform is the enzyme responsible for metabolism of currently available HIV-1 protease drugs. Hence administration of these drugs in HARRT or PI/r leads to increased toxicity and reduced efficacy in HIV treatment. We used computational molecular docking method to predict such interactions by which to compare experimentally measured metabolism of each HIV-1 protease drug. AutoDock 4.0 was used to carry out molecular docking of 10 HIV-protease drugs into CYP3A4 to explore sites of reaction and interaction energies (i.e., binding affinity) of the complexes. Arg105, Arg106, Ser119, Arg212, Ala370, Arg372, and Glu374 are identified as major drug binding residues, and consistent with previous data of site-directed mutagenesis, crystallography structure, modeling, and docking studies. In addition, our docking results suggested that phenylalanine clusters and heme are also participated in the binding to mediate drug oxidative metabolism. We have shown that HIV-1 protease drugs such as tipranavir, nelfinavir, lopinavir, and atazanavir differ in their binding modes on each other for metabolic clearance in CYP3A4, whereas ritonavir, amprenavir, indinavir, saquinavir, fosamprenavir, and darunavir share the same binding mode.

Insight into residues involved in the structure and function of the breast cancer associated protein human gamma synuclein

Aberrantly expressed human gamma synuclein (SNCG) interacts with BubR1 and heat shock protein 70 (Hsp70) in late stages of breast and ovarian cancer. This interaction is essential for progression, development and survival of cancer cells. A short, synthetically designed ankyrin-repeat-containing peptide (ANK peptide) was proven to inhibit the activity of SNCG. However, the potential binding site residues of SNCG responsible for its oncogenic function have not been reported so far. The objectives of this study were to generate a three-dimensional model of SNCG and to identify the key residues involved in interaction with BubR1, ANK peptide and Hsp70. Our study is the first attempt to report the specific binding of SNCG with the TPR motif of BubR1 and the 18kDa region of Hsp70. Our findings provide novel insights into the mechanism of interaction of SNCG, and can act as a basis for the ongoing drug design and discovery process aimed at treating breast and ovarian cancer.

Design, synthesis, molecular docking, and biological evaluation of N-methyl-3-nitro-4-(nitromethyl)-4H-chromen-2-amine derivatives as potential anti-cancer agents

A series of N-methyl-3-nitro-4-(nitromethyl)-4H-chromen-2-amine derivatives 8 were synthesized from 2-((E)-2-nitrovinyl)phenol 7 and ((E)-N-methyl)-1-(methylthio)-2-nitroethenamine 5. The cytotoxic activity of these molecules was tested against two cancer cell lines namely HeLa (cervical cancer) and HEp-2 (epidermoid laryngeal carcinoma). Among them, two molecules (4H-chromenes 8h and 8i) displayed potent anti-proliferative activity with IC50 values of 115.04 and 18.96xa0μM for HeLa and 86.94 and 25.08xa0μM for Hep-2 cell lines, respectively. Morphological evaluation of the cell lines revealed that both 8h and 8i induce the apoptotic process. Molecular docking studies of all the 4H-chromenes 8 with anti-apoptotic Bcl-2, Bcl-w, and Bcl-xL proteins revealed that the 4H-chromenes 8h and 8i have good docking score and thus corroborated in vitro studies. Furthermore, evaluation of Lipinski and ADMET properties revealed their drug-like pharmacokinetic profiles. Thus, 4H-chromenes 8h and 8i exhibit promising anti-cancer properties and can be used as lead compounds for further development.

Synthesis, in vitro and in silico anti-proliferative activity of 4-aryl-4H-chromene derivatives

Abstract A new series of C4-N,N-dialkylaniline-substituted 4-aryl-4H-chromenes were synthesized, and their anti-proliferative properties were evaluated against human cancer cell lines, namely, laryngeal carcinoma (Hep2), lung adenocarcinoma (A549), and cervical cancer (HeLa). The best among them, the 4-aryl-4H-chromene with C4-1-phenylpiperidine substitution was selected for further structure activity relationship (SAR) studies. Among the derivatives, N,6-dimethyl-3-nitro-4-(4-(piperidine-1-yl)phenyl)-4H-chromene-2-amine 3k showed most potent cytotoxic activity against all three cancer cell lines. Toxicity studies revealed that the 4-aryl-4H-chromenes specifically target the cancer cell lines. Molecular docking studies of this compound revealed its efficient interaction with the active site of αβ-tubulin protein.

Design, synthesis, in vitro and in silico anti-cancer activity of 4H-chromenes with C4-active methine groups

A combinatorial library of eighteen C4-active methine-substituted 4H-chromenes were synthesized, and their anti-cancer properties were evaluated against four human cancer cell lines, namely laryngeal carcinoma (Hep2), lung adenocarcinoma (A549), colon carcinoma (HT-29) and cervical cancer (HeLa). Out of them, six displayed significant anti-proliferative activity. The best among them, the 4H-chromene with C4-malononitrile substitution, was selected for further structure–activity relationship studies. Six analogues were synthesized and subjected to in vitro studies on above four cancer cell lines. The best among them was subjected to detail in silico studies by binding with Bcl-2 protein, and the results corroborated those obtained from in vitro studies. Our findings show that the C4-malononitrile and C2-N-phenyl-substituted 4H-chromene are the most promising lead molecules for treatment of cancer.

Synthesis and in silico evaluation of 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives against Alzheimer disease: to understand their interacting mechanism with acetylcholinesterase

Anomalous action of human acetylcholinesterase (hAChE) in Alzheimer’s disease (AD) was restrained by various AChE inhibitors, of which the specific and potent lead candidate Donepezil is used for treating the disease AD. Besides the specificity, the observed undesirable side effects caused by Donepezil invoked the quest for new lead molecules with the increased potency and specificity for AChE. The present study elucidates the potency of six 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives to form a specific interaction with the peripheral anionic site and catalytic anionic subsite residues of hAChE. The NMSMs were prepared in good yield from 1,1-di(methylsulfanyl)-2-nitroethylene and primary amine (or) amino acid esters. In silico interaction analysis reveals specific and potent interactions between hAChE and selected ligand molecules. The site-specific interactions formed between these molecules also results in a conformational change in the orientation of active site residues of hAChE, which prevents them from being accessed by beta-amyloid protein (Aβ), which is a causative agent for amyloid plaque formation and acetylcholine (ACh). In silico interaction analysis between the ligand-bounded hAChE with Aß and ACh confirms this observation. The variation in the conformation of hAChE associated with the decreased ability of Aβ and ACh to access the respective functional residues of hAChE induced by the novel NMSMs favors their selection for in vivo analysis to present themselves as new members of hAChE inhibitors.

6,8-Dichloro-N-methyl-3-nitro-4-nitro­methyl-4H-chromen-2-amine

In the title compound, C11H9Cl2N3O5, the dihydropyran ring adopts a near-half-chair conformation. The benzene ring makes a torsion angle of 5.02u2005(5)° with the dihydropyran ring. Adjacent molecules are interlinked through intermolecular C—H⋯O, N—H⋯O and C—Cl⋯π [3.4743u2005(9)u2005Å] interactions. The intermolecular N—H⋯O hydrogen bond generates an R 2 2(12) motif, which is observed to contribute to the crystal packing stability. Moreover, the molecular structure displays an S(6) motif formed by intramolecular N—H⋯O hydrogen bonding.

3-(4-Methyl­phen­yl)-1-phenyl-3-(4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one

In the title compound, C22H22N2OSe, the fused six-membered ring of the 4,5,6,7-tetrahydrobenzo[d][1,2,3] selenadiazole group adopts a near to envelope (E form) conformation and the five-membered 1,2,3-selenadiazole ring is essentially planar (r.m.s. deviation = 0.0059u2005Å). In the crystal, adjacent molecules are interlinked through weak intermolecular C—H⋯π interactions.

6-Ethyl-N-methyl-3-nitro-4-nitro­methyl-4H-chromen-2-amine

In the title compound, C13H15N3O5, the O and N atoms of the nitromethyl group and the methyl C atom of the ethyl group are disordered over two sets of sites with refined occupancies of 0.629u2005(7):0.371u2005(7) and 0.533u2005(8):0.467u2005(8), respectively. The dihydropyran ring has an extremely flattened conformation. An intramolecular N—H⋯O hydrogen bond occurs. In the crystal, pairs of N—H⋯O hydrogen bonds link molecules, forming inversion dimers. In addition, weak intermolecular C—H⋯O hydrogen bonds are also present.