Papers by Sidhartha Chaudhury
Journal of neurochemistry, Jan 7, 2015
Polysialic acid (PSA), a large, linear glycan composed of 8 to over 100 α2,8-linked sialic acid r... more Polysialic acid (PSA), a large, linear glycan composed of 8 to over 100 α2,8-linked sialic acid residues, modulates development of the nervous system by enhancing cell migration, axon pathfinding, synaptic targeting and by regulating differentiation of progenitor cells. PSA also functions in developing and adult immune systems and is a signature of many cancers. In this study we identified vinorelbine, a semi-synthetic third generation vinca alkaloid, and epirubicin, an anthracycline and 4'-epimer of doxorubicin, as PSA mimetics. Similar to PSA, vinorelbine and epirubicin bind to the PSA-specific monoclonal antibody 735 and compete with the bacterial analogue of PSA, colominic acid in binding to monoclonal antibody 735. Vinorelbine and epirubicin stimulate neurite outgrowth of cerebellar neurons via the neural cell adhesion molecule (NCAM), via myristoylated alanine-rich C kinase substrate, and via fibroblast growth factor receptor, signaling through Erk pathways. Furthermore, t...
Combining computational biology and experimental immunology is a very promising approach to ident... more Combining computational biology and experimental immunology is a very promising approach to identify immune correlates and rational vaccine design
Human Vision and Electronic Imaging X, 2005
People are able to walk without vision to previously viewed targets in the real world. This abili... more People are able to walk without vision to previously viewed targets in the real world. This ability to update one"s position in space has been attributed to a path integration system that uses internally generated self-motion signals together with the perceived object-to-self distance of the target. In a previous study using an immersive virtual environment (VE), we found that many
Journal of immunology (Baltimore, Md. : 1950), 2014
Polyvalent vaccines use a mixture of Ags representing distinct pathogen strains to induce an immu... more Polyvalent vaccines use a mixture of Ags representing distinct pathogen strains to induce an immune response that is cross-reactive and protective. However, such approaches often have mixed results, and it is unclear how polyvalency alters the fine specificity of the Ab response and what those consequences might be for protection. In this article, we present a coarse-grain theoretical model of B cell affinity maturation during monovalent and polyvalent vaccinations that predicts the fine specificity and cross-reactivity of the Ab response. We stochastically simulate affinity maturation using a population dynamics approach in which the host B cell repertoire is represented explicitly, and individual B cell subpopulations undergo rounds of stimulation, mutation, and differentiation. Ags contain multiple epitopes and are present in subpopulations of distinct pathogen strains, each with varying degrees of cross-reactivity at the epitope level. This epitope- and strain-specific model of ...
Journal of chromatography. B, Biomedical sciences and applications, Jan 16, 1999
A supercritical fluid extraction (SFE) method for the extraction of bile acids from faeces is des... more A supercritical fluid extraction (SFE) method for the extraction of bile acids from faeces is described. HPLC with pulsed amperometric detection was used to examine and confirm the recovery of bile acids. The analytes were extracted within a period of 75 min using supercritical carbon dioxide at a pressure of 34.5 MPa and a temperature of 90 degrees C. In developing this method the following parameters were investigated: temperature, pressure, and extraction time. Two alternative methods of sample preparation were also investigated with a view to reducing the overall analysis time. The method was validated for the major primary and secondary bile acids found in faeces. It was found that the overall mean +/- SD recoveries were 102.1+/-7.92%, 111.6+/-9.91%, 112.1+/-9.92% and 113.7+/-9.92% for dry samples and 108.5+/-15.77%, 110.0+/-7.22%, 115.9+/-11.11% and 106.6+/-9.16% for wet samples with respect to cholic, deoxycholic, chenodeoxycholic and lithocholic acid. The SFE is an alternati...
Proteins: Structure, Function, and Bioinformatics, 2010
In CAPRI rounds 13-19, the most native-like structure predicted by RosettaDock resulted in two hi... more In CAPRI rounds 13-19, the most native-like structure predicted by RosettaDock resulted in two high, one medium, and one acceptable ac- curacy model out of 13 targets. The current rounds of CAPRI were especially challenging with many unbound and homology modeled starting structures. Novel docking methods, including EnsembleDock and SnugDock, allowed backbone conformational sampling dur- ing docking and enabled the
Structure, 2009
Drug-resistant mutations (DRMs) in HIV-1 protease are a major challenge to antiretroviral therapy... more Drug-resistant mutations (DRMs) in HIV-1 protease are a major challenge to antiretroviral therapy. Protease-substrate interactions that are determined to be critical for native selectivity could serve as robust targets for drug design that are immune to DRMs. In order to identify the structural mechanisms of selectivity, we developed a peptide docking algorithm to predict the atomic structure of protease-substrate complexes and applied it to a large and diverse set of cleavable and noncleavable peptides. Cleavable peptides showed significantly lower energies of interaction than noncleavable peptides with six protease active-site residues playing the most significant role in discrimination. Surprisingly, all six residues correspond to sequence positions associated with drug resistance mutations, demonstrating that the very residues that are responsible for native substrate specificity in HIV-1 protease are altered during its evolution to drug resistance, suggesting that drug resistance and substrate selectivity may share common mechanisms.
Proteins: Structure, Function, and Bioinformatics, 2009
High-resolution homology models are useful in structure-based protein engineering applications, e... more High-resolution homology models are useful in structure-based protein engineering applications, especially when a crystallographic structure is unavailable. Here, we report the development and implementation of RosettaAntibody, a protocol for homology modeling of antibody variable regions. The protocol combines comparative modeling of canonical complementarity determining region (CDR) loop conformations and de novo loop modeling of CDR H3 conformation with simultaneous optimization of V(L)-V(H) rigid-body orientation and CDR backbone and side-chain conformations. The protocol was tested on a benchmark of 54 antibody crystal structures. The median root mean square deviation (rmsd) of the antigen binding pocket comprised of all the CDR residues was 1.5 A with 80% of the targets having an rmsd lower than 2.0 A. The median backbone heavy atom global rmsd of the CDR H3 loop prediction was 1.6, 1.9, 2.4, 3.1, and 6.0 A for very short (4-6 residues), short (7-9), medium (10-11), long (12-14) and very long (17-22) loops, respectively. When the set of ten top-scoring antibody homology models are used in local ensemble docking to antigen, a moderate-to-high accuracy docking prediction was achieved in seven of fifteen targets. This success in computational docking with high-resolution homology models is encouraging, but challenges still remain in modeling antibody structures for sequences with long H3 loops. This first large-scale antibody-antigen docking study using homology models reveals the level of "functional accuracy" of these structural models toward protein engineering applications.
Proteins: Structure, Function, and Bioinformatics, 2007
In CAPRI rounds 6-12, RosettaDock successfully predicted 2 of 5 unboundunbound targets to medium ... more In CAPRI rounds 6-12, RosettaDock successfully predicted 2 of 5 unboundunbound targets to medium accuracy. Improvement over the previous method was achieved with computational mutagenesis to select decoys that match the energetics of experimentally determined hot spots. In the case of Target 21, Orc1/ Sir1, this resulted in a successful docking prediction where RosettaDock alone or with simple site constraints failed. Experimental information also helped limit the interacting region of TolB/Pal, producing a successful prediction of Target 26. In addition, we docked multiple loop conformations for Target 20, and we developed a novel flexible docking algorithm to simultaneously optimize backbone conformation and rigid-body orientation to generate a wide diversity of conformations for Target 24. Continued challenges included docking of homology targets that differ substantially from their template (sequence identity <50%) and accounting for large conformational changes upon binding. Despite a larger number of unbound-unbound and homology model binding targets, Rounds 6-12 reinforced that RosettaDock is a powerful algorithm for predicting bound complex structures, especially when combined with experimental data. Proteins 2007; 69:793-800. V V C 2007 Wiley-Liss, Inc.
PLoS ONE, 2013
In the future, we may be faced with the need to provide treatment for an emergent biological thre... more In the future, we may be faced with the need to provide treatment for an emergent biological threat against which existing vaccines and drugs have limited efficacy or availability. To prepare for this eventuality, our objective was to use a metabolic network-based approach to rapidly identify potential drug targets and prospectively screen and validate novel smallmolecule antimicrobials. Our target organism was the fully virulent Francisella tularensis subspecies tularensis Schu S4 strain, a highly infectious intracellular pathogen that is the causative agent of tularemia and is classified as a category A biological agent by the Centers for Disease Control and Prevention. We proceeded with a staggered computational and experimental workflow that used a strain-specific metabolic network model, homology modeling and X-ray crystallography of protein targets, and ligand-and structure-based drug design. Selected compounds were subsequently filtered based on physiological-based pharmacokinetic modeling, and we selected a final set of 40 compounds for experimental validation of antimicrobial activity. We began screening these compounds in whole bacterial cell-based assays in biosafety level 3 facilities in the 20th week of the study and completed the screens within 12 weeks. Six compounds showed significant growth inhibition of F. tularensis, and we determined their respective minimum inhibitory concentrations and mammalian cell cytotoxicities. The most promising compound had a low molecular weight, was non-toxic, and abolished bacterial growth at 13 mM, with putative activity against pantetheine-phosphate adenylyltransferase, an enzyme involved in the biosynthesis of coenzyme A, encoded by gene coaD. The novel antimicrobial compounds identified in this study serve as starting points for lead optimization, animal testing, and drug development against tularemia. Our integrated in silico/ in vitro approach had an overall 15% success rate in terms of active versus tested compounds over an elapsed time period of 32 weeks, from pathogen strain identification to selection and validation of novel antimicrobial compounds. Citation: Chaudhury S, Abdulhameed MDM, Singh N, Tawa GJ, D'haeseleer PM, et al. (2013) Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction. PLoS ONE 8(5): e63369.
PLoS ONE, 2013
Vaccine development efforts will be guided by algorithms that predict immunogenic epitopes. Such ... more Vaccine development efforts will be guided by algorithms that predict immunogenic epitopes. Such prediction methods rely on classification-based algorithms that are trained against curated data sets of known B and T cell epitopes. It is unclear whether this empirical approach can be applied prospectively to predict epitopes associated with protective immunity for novel antigens. We present a comprehensive comparison of in silico B and T cell epitope predictions with in vivo validation using an previously uncharacterized malaria antigen, CelTOS. CelTOS has no known conserved structural elements with any known proteins, and thus is not represented in any epitope databases used to train prediction algorithms. This analysis represents a blind assessment of this approach in the context of a novel, immunologically relevant antigen. The limited accuracy of the tested algorithms to predict the in vivo immune responses emphasizes the need to improve their predictive capabilities for use as tools in vaccine design. Citation: Bergmann-Leitner ES, Chaudhury S, Steers NJ, Sabato M, Delvecchio V, et al. (2013) Computational and Experimental Validation of B and T-Cell Epitopes of the In Vivo Immune Response to a Novel Malarial Antigen. PLoS ONE 8(8): e71610.
PLoS Computational Biology, 2012
Quantitatively predicting changes in drug sensitivity associated with residue mutations is a majo... more Quantitatively predicting changes in drug sensitivity associated with residue mutations is a major challenge in structural biology. By expanding the limits of free energy calculations, we successfully identified mutations in influenza neuraminidase (NA) that confer drug resistance to two antiviral drugs, zanamivir and oseltamivir. We augmented molecular dynamics (MD) with Hamiltonian Replica Exchange and calculated binding free energy changes for H274Y, N294S, and Y252H mutants. Based on experimental data, our calculations achieved high accuracy and precision compared with results from established computational methods. Analysis of 15 ms of aggregated MD trajectories provided insights into the molecular mechanisms underlying drug resistance that are at odds with current interpretations of the crystallographic data. Contrary to the notion that resistance is caused by mutant-induced changes in hydrophobicity of the binding pocket, our simulations showed that drug resistance mutations in NA led to subtle rearrangements in the protein structure and its dynamics that together alter the active-site electrostatic environment and modulate inhibitor binding. Importantly, different mutations confer resistance through different conformational changes, suggesting that a generalized mechanism for NA drug resistance is unlikely.
Journal of cheminformatics, 2012
ABSTRACT:
Neuropharmacology, 2014
Glycans attached to the cell surface via proteins or lipids or exposed in the extracellular matri... more Glycans attached to the cell surface via proteins or lipids or exposed in the extracellular matrix affect many cellular processes, including neuritogenesis, cell survival and migration, as well as synaptic activity and plasticity. These functions make glycans attractive molecules for stimulating repair of the injured nervous system. Yet, glycans are often difficult to synthesize or isolate and have the disadvantage to be unstable in a complex tissue environment. To circumvent these issues, we have screened a library of small organic compounds to search for structural and functional mimetics of the neurostimulatory glycan polysialic acid (PSA) and identified the 5-HT4 receptor agonist tegaserod as a PSA mimetic. The PSA mimicking activity of tegaserod was shown in cultures of central and peripheral nervous system cells of the mouse and found to be independent of its described function as a serotonin (5-HT4) receptor agonist. In an in vivo model for peripheral nerve regeneration, mice receiving tegaserod at the site of injury showed enhanced recovery compared to control mice receiving vehicle control as evidenced by functional measurements and histology. These data indicate that tegaserod could be repurposed for treatment of nervous system injuries and underscores the potential of using small molecules as mimetics of neurostimulatory glycans.
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Papers by Sidhartha Chaudhury