A Swift All-Atom Energy-Based Computational Protocol to Predict DNA−Ligand Binding Affinity and ΔTm

Marshall's nucleic acid: From double-helical structure to a potent intercalator

Deoxyribonucleic acid (DNA) not only stores genetic information but also emerged as a popular drug target. Modified nucleotides/nucleosides have been extensively studied in recent years wherein the sugar/nucleobase/phosphate-backbone has been altered. Several such molecules are FDA approved, capable of targeting nucleic acids and proteins. In this article, we modified negatively charged phosphate backbone to marshall's acid-based neutral backbone and analyzed the resultant structures by utilizing Gaussian accelerated molecular dynamics simulations (1 μs) in aqueous media at 150 mM salt concentration. We noted that the double-helical marshall's nucleic acid structure was partially denatured during the course of simulations, however, after using conformationally locked sugar, the marshall's nucleic acid (hereby called MNA) maintained the double-helical structure throughout the simulations. Despite the fact that MNA has a more extended backbone than the regular DNA, surprisingly, both showed similar helical rise (~3.4 Å) along with a comparable Watson-Crick hydrogen bond profile. The backbone difference was majorly compensated in terms of helical twist (~56° (MNA) and ~ 35° (control DNA)). Further, we examined a few MNA based ss-dinucleotides as intercalating ligands for a regular B-DNA. Quite strikingly, the ligands unwinded the DNA and showed intercalating properties with high DNA binding affinities. Hence, the use of small fragments of MNA based molecules in DNA targeted drug discovery is foreseen.

An in-silico layer-by-layer adsorption study of the interaction between Rebaudioside A and the T1R2 human sweet taste receptor: modelling and biosensing perspectives

The human sweet taste receptor (T1R2) monomer-a member of the G-protein coupled receptor family that detects a wide variety of chemically and structurally diverse sweet tasting molecules, is known to pose a significant threat to human health. Protein that lack crystal structure is a challenge in structure-based protein design. This study focused on the interaction of the T1R2 monomer with rebaudioside A (Reb-A), a steviol glycoside with potential use as a natural sweetener using in-silico and biosensing methods. Herein, homology modelling, docking studies, and molecular dynamics simulations were applied to elucidate the interaction between Reb-A and the T1R2 monomer. In addition, the electrochemical sensing of the immobilised T1R2-Reb-A complex with zinc oxide nanoparticles (ZnONPs) and graphene oxide (GO) were assessed by testing the performance of multiwalled carbon nanotube (MWCNT) as an adsorbent experimentally. Results indicate a strong interaction between Reb-A and the T1R2 receptor, revealing the stabilizing interaction of the amino acids with the Reb-A by hydrogen bonds with the hydroxyl groups of the glucose moieties, along with a significant amount of hydrophobic interactions. Moreover, the presence of the MWCNT as an anchor confirms the adsorption strength of the T1R2-Reb-A complex onto the GO nanocomposite and supported with electrochemical measurements. Overall, this study could serve as a cornerstone in the development of electrochemical immunosensor for the detection of Reb-A, with applications in the food industry.

Comparative in silico study of congocidine congeners as potential inhibitors of African swine fever virus

African swine fever virus (ASFV) infection is fatal in domesticated pigs, with a mortality rate approaching 100%. This may result in economic losses and threats to food security. Currently, there are no approved vaccines or antiviral therapies for ASFV. Therefore, in this study, we evaluated congocidine congeners and a tris-benzimidazole as potential inhibitors of ASFV transcription using an in silico approach. We applied redocking of congocidine and docking of its congeners and a tris-benzimidazole to a receptor containing B-DNA with AT-motifs as a target to mimic conserved ASFV late gene promoters. Subsequently, the binding scores of DNA-ligand docked complexes were evaluated and their binding affinity was estimated. Molecular dynamics (MD) simulation was then used to assess ligand behavior within the minor groove. From our results, it is evident the less toxic congocidine congeners and tris-benzimidazole could dock to AT-rich regions significantly. Additionally, the predicted binding affinities had suitable values comparable to other experimentally determined minor groove binders, MD simulation of the docked DNA-ligand complexes and subsequent molecular trajectory visualization further showed that the ligands remained embedded in the minor groove during the time course of simulation, indicating that these ligands may have potential applications in abrogating ASFV transcription.

Synergistic enhancement of apoptosis by coralyne and paclitaxel in combination on MDA-MB-231 a triple-negative breast cancer cell line

Triple-negative breast cancer (TNBC) is the most outrageous subtype of breast cancer. Emphasizing the urge of new approach in cancer therapy, combinational drug therapy may be proven as an effective strategy. In our previous study, we reported that coralyne (COR) with paclitaxel (PTX) efficiently decreases the proliferation of MDA-MB-231 compared with MCF-7 cell line. Thus, we studied the effect of COR and PTX in combination on apoptosis of MDA-MB-231 cell line. In silico results demonstrated that COR intercalates DNA at a minor groove. In vitro approaches revealed that in combination (COR and PTX) increases the efficacy of apoptosis in MDA-MB-231 cell line by a significant increase in G1/S phase arrest, DNA fragmentation, and change in mitochondria membrane potential. The expression of ATM and ATR a serine/threonine-protein kinase, ataxia telangiectasia and Rad3-related protein were depleted with an increase in time from 24 to 48 hours in concurrent with increased levels of γH2AX indicating that DNA damage routes cells to enter apoptosis. This was confirmed by high levels of caspase-3 and cytochrome c. Also, the decrease in the expression levels of matrix metalloproteinase-9 confirmed the antimetastatic efficacy of COR + PTX. The present study indicates that the synergistic effect of COR and PTX can enhance apoptosis in MDA-MB-231 cell line and may be proven as a potential anticancer therapy against TNBC.

Computational Approaches to Matrix Metalloprotease Drug Design

Matrix metalloproteinases (MMPs) are a family of zinc-containing enzymes required for homeostasis. These enzymes are an important class of drug targets as their over expression is associated with many disease states. Most of the inhibitors reported against this class of proteins have failed in clinical trials due to lack of specificity. In order to assist in drug design endeavors for MMP targets, a computationally tractable pathway is presented, comprising, (1) docking of small molecule inhibitors against the target MMPs, (2) derivation of quantum mechanical charges on the zinc ion in the active site and the amino acids coordinating with zinc including the inhibitor molecule, (3) molecular dynamics simulations on the docked ligand-MMP complexes, and (4) evaluation of binding affinities of the ligand-MMP complexes via an accurate scoring function for zinc containing metalloprotein-ligand complexes. The above pathway was applied to study the interaction of the inhibitor Batimastat with MMPs, which resulted in a high correlation between the predicted and experimental binding free energies, suggesting the potential applicability of the pathway.

A computational protocol for the discovery of lead molecules targeting DNA unique to pathogens

With the rapid emergence of drug resistant pathogens, it has become imperative to develop alternative medications as well as find new drug targets to overcome this crisis. Hence, this has become prime focus of several academic laboratories and pharmaceutical companies. Here, we report a computational protocol for identifying unique DNA sequence(s) in the pathogen which is absent in human and related non-pathogenic strains of the microbe. In order to use the unique sequence as drug target, the protocol, in the second step, uses virtual screening against a million compound library to identify candidate small molecules which can bind to these unique DNA targets in the pathogen only. Theoretically the molecules identified after screening should not bind to human DNA. This methodology is demonstrated on Mycobacterium tuberculosis H37Rv, wherein a new octamer sequence present only in H37Rv has been identified and a few candidate small molecules as potential drug have been proposed. Being fast and cost effective, this protocol could be of importance in generating new potential drug candidates against infectious organisms for further experimental studies. This methodology is freely available at http://www.scfbio-iitd.res.in/PSDDF/.

Design and characterization of symmetric nucleic acids via molecular dynamics simulations

Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C_3' to C_2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C_5' to C_2' ) can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations.

Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes

Transcription factors (TFs) bind at multiple sites in the genome and regulate expression of many genes. Regulating TF binding in a gene specific manner remains a formidable challenge in drug discovery because the same binding motif may be present at multiple locations in the genome. Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome. USP works by extending a given DNA motif, in 5′→3′, 3′ →5′ or both directions by adding one nucleotide at each step, and calculates the frequency of each extended motif in the genome by Frequency Counter programme. This step is iterated till the frequency of the extended motif becomes unity in the genome. Thus, for each given motif, we get three possible unique sequences. Closest Sequence Finder program predicts off-target drug binding in the genome. Inclusion of DNA-Protein structural information further makes Onco-Regulon a highly informative repository for gene specific drug development. We believe that Onco-Regulon will help researchers to design drugs which will bind to an exclusive site in the genome with no off-target effects, theoretically.

Database URL:http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm

Binding Free Energy Calculations of Nine FDA-approved Protease Inhibitors Against HIV-1 Subtype C I36T↑T Containing 100 Amino Acids Per Monomer

In this work, have investigated the binding affinities of nine FDA-approved protease inhibitor drugs against a new HIV-1 subtype C mutated protease, I36T↑T. Without an X-ray crystal structure, homology modelling was used to generate a three-dimensional model of the protease. This and the inhibitor models were employed to generate the inhibitor/I36T↑T complexes, with the relative positions of the inhibitors being superimposed and aligned using the X-ray crystal structures of the inhibitors/HIV-1 subtype B complexes as a reference. Molecular dynamics simulations were carried out on the complexes to calculate the average binding free energies for each inhibitor using the molecular mechanics generalized Born surface area (MM-GBSA) method. When compared to the binding free energies of the HIV-1 subtype B and subtype C proteases (calculated previously by our group using the same method), it was clear that the I36T↑T proteases mutations and insertion had a significant negative effect on the binding energies of the non-pepditic inhibitors nelfinavir, darunavir and tipranavir. On the other hand, ritonavir, amprenavir and indinavir show improved calculated binding energies in comparison with the corresponding data for wild-type C-SA protease. The computational model used in this study can be used to investigate new mutations of the HIV protease and help in establishing effective HIV drug regimes and may also aid in future protease drug design.

Cation–π interactions in CREBBP bromodomain inhibition: an electrostatic model for small-molecule binding affinity and selectivity

A new model is presented to explain and predict binding affinity of aromatic and heteroaromatic ligands for the CREBBP bromodomain based on cation–π interaction strength.

Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study

Matrix metalloproteinases (MMPs) consist of a class of proteins required for normal tissue function. Their over expression is associated with many disease states and hence the interest in MMPs as drug targets. Almost all MMP inhibitors have been reported to fail in clinical trials due to lack of specificity. Zinc in the binding site of metalloproteinases performs essential biological functions and contributes to the binding affinity of inhibitors. The multiple possibilities for coordination geometry and the consequent charge on the zinc atom indicate that parameters developed are not directly transferable across different families of zinc metalloproteinases with different zinc coordination geometries, active sites and ligand architectures which makes it difficult to evaluate metal-ligand interactions. In order to assist in drug design endeavors for MMP targets, a computationally tractable pathway is presented, comprising docking of small molecule inhibitors against the target MMPs, derivation of quantum mechanical charges on the zinc ion in the active site and the amino acids coordinating with zinc including the inhibitor molecule, molecular dynamics simulations on the docked ligand-MMP complexes and evaluation of binding affinities of the ligand-MMP complexes via an accurate scoring function for zinc containing metalloprotein-ligand complexes. The above pathway was applied to study the interaction of inhibitor Batimastat with MMPs, which resulted in a high correlation between the predicted binding free energies and experiment, suggesting the potential applicability of the pathway. We then proceeded to formulate a few design principles which identify the key protein residues for generating molecules with high affinity and specificity against each of the MMPs.

The impact of active site mutations of South African HIV PR on drug resistance: Insight from molecular dynamics simulations, binding free energy and per-residue footprints

Molecular dynamics simulations and binding free energy calculations were used to provide an understanding of the impact of active site drug-resistant mutations of the South African HIV protease subtype C (C-SA HIV PR), V82A and V82F/I84V on drug resistance. Unique per-residue interaction energy 'footprints' were developed to map the overall drug-binding profiles for the wild type and mutants. Results confirmed that these mutations altered the overall binding landscape of the amino acid residues not only in the active site region but also in the flaps as well. Four FDA-approved drugs were investigated in this study; these include ritonavir (RTV), saquinavir (SQV), indinavir (IDV), and nelfinavir (NFV). Computational results compared against experimental findings were found to be complementary. Against the V82F/I84V variant, saquinavir, indinavir, and nelfinavir lose remarkable entropic contributions relative to both wild-type and V82A C-SA HIV PRs. The per-residue energy 'footprints' and the analysis of ligand-receptor interactions for the drug complexes with the wild type and mutants have also highlighted the nature of drug interactions. The data presented in this study will prove useful in the design of more potent inhibitors effective against drug-resistant HIV strains.

Bio/chemoinformatics in India: an outlook

With the advent of significant establishment and development of Internet facilities and computational infrastructure, an overview on bio/chemoinformatics is presented along with its multidisciplinary facts, promises and challenges. The Government of India has paved the way for more profound research in biological field with the use of computational facilities and schemes/projects to collaborate with scientists from different disciplines. Simultaneously, the growth of available biomedical data has provided fresh insight into the nature of redundant and compensatory data. Today, bioinformatics research in India is characterized by a powerful grid computing systems, great variety of biological questions addressed and the close collaborations between scientists and clinicians, with a full spectrum of focuses ranging from database building and methods development to biological discoveries. In fact, this outlook provides a resourceful platform highlighting the funding agencies, institutes and industries working in this direction, which would certainly be of great help to students seeking their career in bioinformatics. Thus, in short, this review highlights the current bio/chemoinformatics trend, educations, status, diverse applicability and demands for further development.

Proceedings of the Indo-U.S. bilateral workshop on accelerating botanicals/biologics agent development research for cancer chemoprevention, treatment, and survival

With the evolving evidence of the promise of botanicals/biologics for cancer chemoprevention and treatment, an Indo-U.S. collaborative Workshop focusing on “Accelerating Botanicals Agent Development Research for Cancer Chemoprevention and Treatment” was conducted at the Moffitt Cancer Center, 29–31 May 2012. Funded by the Indo-U.S. Science and Technology Forum, a joint initiative of Governments of India and the United States of America and the Moffitt Cancer Center, the overall goals of this workshop were to enhance the knowledge (agents, molecular targets, biomarkers, approaches, target populations, regulatory standards, priorities, resources) of a multinational, multidisciplinary team of researcher's to systematically accelerate the design, to conduct a successful clinical trials to evaluate botanicals/biologics for cancer chemoprevention and treatment, and to achieve efficient translation of these discoveries into the standards for clinical practice that will ultimately impact cancer morbidity and mortality. Expert panelists were drawn from a diverse group of stakeholders, representing the leadership from the National Cancer Institute's Office of Cancer Complementary and Alternative Medicine (OCCAM), NCI Experimental Therapeutics (NExT), Food and Drug Administration, national scientific leadership from India, and a distinguished group of population, basic and clinical scientists from the two countries, including leaders in bioinformatics, social sciences, and biostatisticians. At the end of the workshop, we established four Indo-U.S. working research collaborative teams focused on identifying and prioritizing agents targeting four cancers that are of priority to both countries. Presented are some of the key proceedings and future goals discussed in the proceedings of this workshop.

Bi and tri-substituted phenyl rings containing bisbenzimidazoles bind differentially with DNA duplexes: a biophysical and molecular simulation study

Recently synthesis of programmable DNA ligands which can regulate transcription factors have increased the interest of researchers on the functional ability of DNA interacting compounds. A series of DNA interacting compounds are being designed which can differentiate between GC and AT rich DNA. In this study, we have studied the specificity of a few novel bisbenzimidazoles having different bi/tri-substituted phenyl rings, with DNA duplexes using spectroscopic methods. This study entails an integrative approach where we combine biophysical methods and molecular dynamics simulation studies to establish suitable scaffolds to target A/T DNA. We have designed a few analogues of Hoechst 33342 viz.; dimethoxy (DMA), trimethoxy (TMA), dichloro (DCA) and difluoro (DFA) functionalities and performed molecular docking of newly designed analogues with biologically relevant AT and GC rich DNA sequences. The docking studies, along with molecular dynamics (MD) simulations of d(ATATATATATATATAT)2, d(GA4T4C)2, d(GT4A4C)2 and GC rich sequence: d(GCGCGCGCGCGCGCGC)2 complexed with DMA, TMA and DFA, showed that these molecules have higher binding affinity towards AT rich DNA. None of these compounds exhibited an affinity to GC rich DNA rather we observed that these compounds destabilize GC rich DNA. The binding was characterized by strong stabilization of the polynucleotides against thermal strand separation in thermal melting experiments. New insights into the molecules binding to DNA have emerged from these studies. All the DNA binding ligands stabilized d(GA4T4C)2 and d(GT4A4C)2 more out of the five oligomers used for the study, suggesting that these ligands bind 'A4T4' and 'T4A4' strongly as compared to 'ATAT' base pairs.

Genomes to hits in silico - a country path today, a highway tomorrow: a case study of chikungunya

These are exciting times for bioinformaticians, computational biologists and drug designers with the genome and proteome sequences and related structural databases growing at an accelerated pace. The post-genomic era has triggered high expectations for a rapid and successful treatment of diseases. However, in this biological information rich and functional knowledge poor scenario, the challenges are indeed grand, no less than the assembly of the genome of the whole organism. These include functional annotation of genes, identification of druggable targets, prediction of three-dimensional structures of protein targets from their amino acid sequences, arriving at lead compounds for these targets followed by a transition from bench to bedside. We propose here a "Genome to Hits In Silico" strategy (called Dhanvantari) and illustrate it on Chikungunya virus (CHIKV). "Genome to hits" is a novel pathway incorporating a series of steps such as gene prediction, protein tertiary structure determination, active site identification, hit molecule generation, docking and scoring of hits to arrive at lead compounds. The current state of the art for each of the steps in the pathway is high-lighted and the feasibility of creating an automated genome to hits assembly line is discussed.

Sanjeevini: a freely accessible web-server for target directed lead molecule discovery

Background

Computational methods utilizing the structural and functional information help to understand specific molecular recognition events between the target biomolecule and candidate hits and make it possible to design improved lead molecules for the target.

Results

Sanjeevini represents a massive on-going scientific endeavor to provide to the user, a freely accessible state of the art software suite for protein and DNA targeted lead molecule discovery. It builds in several features, including automated detection of active sites, scanning against a million compound library for identifying hit molecules, all atom based docking and scoring and various other utilities to design molecules with desired affinity and specificity against biomolecular targets. Each of the modules is thoroughly validated on a large dataset of protein/DNA drug targets.

Conclusions

The article presents Sanjeevini, a freely accessible user friendly web-server, to aid in drug discovery. It is implemented on a tera flop cluster and made accessible via a web-interface at http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp. A brief description of various modules, their scientific basis, validation, and how to use the server to develop in silico suggestions of lead molecules is provided.

Structural studies on ligand-DNA systems: A robust approach in drug design

Molecular docking, molecular mechanics, molecular dynamics and relaxation matrix simulation protocols have been extensively used to generate the structural details of ligand-receptor complexes in order to understand the binding interactions between the two entities. Experimental methods like NMR spectroscopy and X-ray crystallography are known to provide structural information about ligand-receptor complexes. In addition, fluorescence spectroscopy, circular dichroism (CD) spectroscopy and molecular docking have also been utilized to decode the phenomenon of the ligand-DNA interactions, with good correlation between experimental and computational results. The DNA binding affinity was demonstrated by analysing fluorescence spectral data. Structural rigidity of DNA upon ligand binding was identified by CD spectroscopy. Docking is carried out using the DNA-Dock program which results in the binding affinity data along with structural information like interatomic distances and H-bonding, etc. The complete structural analyses of various drug-DNA complexes have afforded results that indicate a specific DNA binding pattern of these ligands. It also exhibited that certain structural features of ligands can make a ligand to be AT- or GC-specific. It was also demonstrated that changing specificity from AT base pairs to GC base pairs further improved the DNA topoisomerase inhibiting activity in certain ligands. Thus, a specific molecular recognition signature encrypted in the structure of ligand can be decoded and can be effectively employed in designing more potent antiviral and antitumour agents.

DNA Binding Studies of Vinca Alkaloids: Experimental and Computational Evidence

Fluorescence studies on the indole alkaloids vinblastine sulfate, vincristine sulfate, vincamine and catharanthine have demonstrated the DNA binding ability of these molecules. The binding mode of these molecules in the minor groove of DNA is non-specific. A new parameter of the purine-pyrimidine base sequence specificty was observed in order to define the non-specific DNA binding of ligands. Catharanthine had shown ‘same’ pattern of ‘Pu-Py’ specificity while evaluating its DNA binding profile. The proton resonances of a DNA decamer duplex were assigned. The models of the drug:DNA complexes were analyzed for DNA binding features. The effect of temperature on the DNA binding was also evaluated.

AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors

We report here a robust automated active site detection, docking, and scoring (AADS) protocol for proteins with known structures. The active site finder identifies all cavities in a protein and scores them based on the physicochemical properties of functional groups lining the cavities in the protein. The accuracy realized on 620 proteins with sizes ranging from 100 to 600 amino acids with known drug active sites is 100% when the top ten cavity points are considered. These top ten cavity points identified are then submitted for an automated docking of an input ligand/candidate molecule. The docking protocol uses an all atom energy based Monte Carlo method. Eight low energy docked structures corresponding to different locations and orientations of the candidate molecule are stored at each cavity point giving 80 docked structures overall which are then ranked using an effective free energy function and top five structures are selected. The predicted structure and energetics of the complexes agree quite well with experiment when tested on a data set of 170 protein-ligand complexes with known structures and binding affinities. The AADS methodology is implemented on an 80 processor cluster and presented as a freely accessible, easy to use tool at http://www.scfbio-iitd.res.in/dock/ActiveSite_new.jsp .

Prediction of zanamivir efficiency over the possible 2009 influenza A (H1N1) mutants by multiple molecular dynamics simulations and free energy calculations

As one of the most important antiviral drugs against 2009 influenza A (H1N1), will zanamivir be effective for the possible drug resistant mutants? To answer this question, we combined multiple molecular dynamics simulations and molecular mechanics generalized Born surface area (MM-GBSA) calculations to study the efficiency of zanamivir over the most frequent drug-resistant strains of neuraminidase including R293K, R152K, E119A/D and H275Y mutants. The calculated results indicate that the modeled mutants of the 2009-H1N1 strains except H275Y will be significantly resistant to zanamivir. The resistance to zanamivir is mainly caused by the loss of polar interactions. The identified potential resistance sites in this study will be useful for the development of new effective anti-influenza drugs and to avoid the occurrence of the state without effective drugs to new mutant influenza strains.

Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach

Proper modeling of nonspecific salt-mediated electrostatic interactions is essential to understanding the binding of charged ligands to nucleic acids. Because the linear Poisson-Boltzmann equation (PBE) and the more approximate generalized Born approach are applied routinely to nucleic acids and their interactions with charged ligands, the reliability of these methods is examined vis-à-vis an efficient nonlinear PBE method. For moderate salt concentrations, the negative derivative, SK(pred), of the electrostatic binding free energy, DeltaG(el), with respect to the logarithm of the 1:1 salt concentration, [M(+)], for 33 cationic minor groove drugs binding to AT-rich DNA sequences is shown to be consistently negative and virtually constant over the salt range considered (0.1-0.4 M NaCl). The magnitude of SK(pred) is approximately equal to the charge on the drug, as predicted by counterion condensation theory (CCT) and observed in thermodynamic binding studies. The linear PBE is shown to overestimate the magnitude of SK(pred), whereas the nonlinear PBE closely matches the experimental results. The PBE predictions of SK(pred) were not correlated with DeltaG(el) in the presence of a dielectric discontinuity, as would be expected from the CCT. Because this correlation does not hold, parameterizing the PBE predictions of DeltaG(el) against the reported experimental data is not possible. Moreover, the common practice of extracting the electrostatic and nonelectrostatic contributions to the binding of charged ligands to biopolyelectrolytes based on the simple relation between experimental SK values and the electrostatic binding free energy that is based on CCT is called into question by the results presented here. Although the rigid-docking nonlinear PB calculations provide reliable predictions of SK(pred), at least for the charged ligand-nucleic acid complexes studied here, accurate estimates of DeltaG(el) will require further development in theoretical and experimental approaches.

In silico identification of the potential drug resistance sites over 2009 influenza A (H1N1) virus neuraminidase

The outbreak and high speed global spread of the new strain of influenza A (H1N1) virus in 2009 poses a serious threat to the general population and governments. At present, the most effective drugs for the treatment of 2009 influenza A (H1N1) virus are neuraminidase inhibitors: mainly oseltamivir and zanamivir. The use of these two inhibitors will undoubtedly increase, and therefore it is more likely that drug-resistant influenza strains will arise. The identification of the potential resistance sites for these drugs in advance and the understanding of corresponding molecular basis to cause drug resistance are no doubt very important to fight against the new resistant influenza strains. In this study, first, the complexes of neuraminidase with the substrate sialic acid and two inhibitors oseltamivir and zanamivir were obtained by fitting them to the 3D structure of 2009 influenza A (H1N1) neuraminidase obtained by homology modeling. By using these complexes as the initial structures, molecular dynamics simulation and molecular mechanics generalized Born surface area (MM-GBSA) calculations were performed to identify the residues with significant contribution to the binding of substrate and inhibitors. By analyzing the difference of interaction profiles of substrate and inhibitors, the potential drug resistance sites for two inhibitors were identified. Parts of the identified sites have been verified to confer resistance to oseltamivir and zanamivir for influenza virus of the past flu epidemic. The identified potential resistance sites in this study will be useful for the development of new effective drugs against the drug resistance and avoid the situation of having no effective drugs to treat new mutant influenza strains.

A phenomenological model for predicting melting temperatures of DNA sequences

We report here a novel method for predicting melting temperatures of DNA sequences based on a molecular-level hypothesis on the phenomena underlying the thermal denaturation of DNA. The model presented here attempts to quantify the energetic components stabilizing the structure of DNA such as base pairing, stacking, and ionic environment which are partially disrupted during the process of thermal denaturation. The model gives a Pearson product-moment correlation coefficient (r) of approximately 0.98 between experimental and predicted melting temperatures for over 300 sequences of varying lengths ranging from 15-mers to genomic level and at different salt concentrations. The approach is implemented as a web tool (www.scfbio-iitd.res.in/chemgenome/Tm_predictor.jsp) for the prediction of melting temperatures of DNA sequences.