Ramaswamy H. Sarma

Biological Evaluation and Interaction of a Newly Designed Anti-cancer Pd(II) Complex and Human Serum Albumin

Abstract The pharmacokinetics and pharmacodynamics of any drug will depend, largely, on the interaction that has with human serum albumin (HSA), the most abundant plasma protein. The interaction between newly synthesized Pd(II) complexe, 2,2′-bipyridin Butylglycinato Pd(II) nitrate, an anti-tumor component, with HSA was studied at different temperatures by fluorescence, far UV circular dichroism (CD), UV-visible spectrophotometry and theoretical approaches. The Pd(II) complex has a strong ability to quench the intrinsic fluorescence of HSA through a dynamic quenching procedure. The binding parameters and thermodynamic parameters, including ΔH°, ΔS° and ΔG° were calculated by fluorescence quenching method, indicated that hydrophobic forces play a major role in the interaction of Pd(II) complex with HSA. Based on Autodock, FRET (fluorescence resonance energy transfer) and fluorescence quenching data, it may be concluded that one of the binding sites in the complex of HSA is near the only one Trp of HSA (Trp214) in sub domain IIA of the protein. Far-UV-CD results indicated that Pd(II)-complex induced increase in the α-helical content of the protein. The anti-tumor property of the synthesized Pd(II) complex was studied by testing it on human tumor cell line K562. The 50% cytotoxic concentration (Cc50) of complex was determined using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. Also, fluorescence staining with DAPI (4,6-diamidino-2-phenylindole) revealed some typical nuclear changes that are characteristic of apoptosis which is induced at Cc50 concentration of Pd(II) complex in K562 cell line after 24 h incubation. Our results suggest that Pd(II) complex is a promising anti-proliferative agent and should execute its biological effects by inducing apoptosis.

In Search of a Hoogsteen Base Paired DNA Duplex in Aqueous Solution

When the oligodeoxynucleotides d(A)6 and d(T)6 are mixed together in a 1:1 ratio (in 100 mM NaCl), the NH signals in the NMR spectrum gave a typical signature of Watson-Crick paired (WC) and Hoogsteen paired (H) AT base pairs. The observation indicates two schemes: Scheme I, WC and H duplexes in slow equilibrium, i.e., WC in equilibrium with H, Scheme II, the WC helix formed is unstable and that it disproportionates into a triple helix (TR) and free d(A)6. We show that (i) addition of extra d(A)6 does not change the helix composition, (ii) addition of a minor-groove specific drug Dst2 (a distamycin analogue) results in an exclusive WC helix-drug duplex, while it does not destabilize triple helix in a 1:2 mixture. In addition we have compared the melting profile, 31P NMR spectra, 1H NMR spectra and the salt dependence of the 1:1 mixture and that of a pure triple helix. All the data from the above experiments overwhelmingly favor Scheme I. However Scheme II cannot be categorically excluded. Based on 1D/2D NMR studies, we have characterized the structural properties of the Hoogsteen double helix in terms of nucleotide conformations. In addition, we computationally demonstrate that the relative stability of the WC over the H duplexes increases with increasing chain length.

Valery (Chrom) Ivanov in memoriam.

Valery (Chrom) Ivanov In memoriam Maxim Frank-Kamenetskii a , Edward Trifonov b , Victor Zhurkin c , Victor Danilov d , Mukti Sarma e & Ramaswamy Sarma e a Department of Biomedical Engineering, Boston University, Boston, MA, USA b Institute of Evolution, University of Haifa, Haifa, Israel c National Cancer Institute, Bethesda, MD, USA d Institute of Molecular Biology and Genetics of National Academy of Sciences, Kiev, Ukraine e Chemistry Department, State University of New York, Albany, NY, USA Version of record first published: 22 Nov 2012.

Molecular Modeling of a Leishmania Antigen eIF-4A: Identification of a Potential Epitope Implicated in the Adjuvant Effect

Abstract In leishmaniasis, the development of an effective vaccine depends on its capacity to elicit Th1 immune responses. Despite many approaches, recent vaccines do not induce sufficient levels of protection and long-term memory. To overcome this problem, vaccines are used with adjuvants that drive immunity towards Th1 and enhance endogenous production of IL-12, a Th1-promoting cytokine. Although exogenous IL-12 may act as an effective adjuvant, it has an elevated cost and toxic effects. Therefore, it is important to develop cheap and safer adjuvants that trigger endogenous IL-12. Of particular interest is LmeIF a unique Leishmania protein that provides significant adjuvant effects by stimulating high IL-12 production. This investigation was designed to identify the structural factors responsible for the adjuvant effects of LmeIF by establishing the 3D models of LmeIF and MueIF (mouse) by homology modeling based on the X-ray structure of their homologs in yeast and comparing their stereo-electronic properties. The molecular electrostatic potential was computed around each model and used to localize the active site and the most different amino acids between LmeIF and MueIF. Sequence alignment of LmeIF with eIF-4 from other species showed three residues (Q186, A189, E214) in the active site which were peculiar to the Leishmania protein. Long MD simulation was carried out on LmeIF fragment 129–261 to compare its folding with the native protein. Despite a high degree of sequence similarity with different species, we have identified in LmeIF a set of residues unique to the protozoan parasite Leishmania which may be potentially responsible for its adjuvant property. Using LmeIF model, a plausible surface region for binding with its receptor was also identified.

The combined use of 1H and 31P fast Fourier transform nuclear magnetic resonance spectroscopy and line shape computer simulations to determine the torsional diastereomers constrained to the C(5′)–O(5′) bonds of pyridine dinucleotides

A method to determine the torsional diastereomers constrained to the C(5′)–O(5′) bonds of dinucleotides in general, with special reference to pyridine dinucleotides, is described.