Viswa Colluru

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MS2Mol: A transformer model for illuminating dark chemical space from mass spectra

ChemRxiv

Jun 2023

The ability to identify small molecules in complex samples from their mass spectra is among the grand challenges of analytical chemistry. Improvements to this ability could significantly advance fields as diverse as drug discovery, diagnostics, environmental science, and synthetic biology. A primary bottleneck is that standard structure elucidation technologies are limited to identifying only those molecules that are contained in databases of known spectra or molecular structures and are therefore not well suited to identifying the vast majority of potentially billions of natural metabolites, whose structures are not yet catalogued. To improve the identification of molecular structures within this vast dark chemical space, we present MS2Mol

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Mini-intronic plasmid vaccination elicits tolerant LAG3+ CD8 T cells and inferior anti-tumor responses

Oncoimmunology Taylor Francis

Sep 2016

Increasing transgene expression has been a major focus of attempts to improve DNA vaccine-induced immunity in both preclinical studies and clinical trials. Novel mini-intronic plasmids (MIPs) have been shown to cause elevated and sustained transgene expression in vivo. We sought to test the antitumor activity of a mini-intronic plasmid (MIP), compared to standard DNA plasmid immunization, using the tumor-specific antigen SSX2 in an HLA-A2-restricted tumor model. We found that MIP vaccination elicited a greater frequency of antigen-specific CD8 T cells when compared to conventional plasmid, and protected animals from subsequent tumor challenge. However, therapeutic vaccination with the MIP resulted in an inferior antitumor effect, and CD8+ t

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B lymphocytes as direct antigen-presenting cells for anti-tumor DNA vaccines.

Oncotarget Impact Journals

Sep 2016

In spite of remarkable preclinical efficacy, DNA vaccination has demonstrated low immunogenicity in humans. While efforts have focused on increasing cross-presentation of DNA-encoded antigens, efforts to increase DNA vaccine immunogenicity by targeting direct presentation have remained mostly unexplored. In these studies, we compared the ability of different APCs to present antigen to T cells after simple co-culture with plasmid DNA. We found that human primary peripheral B lymphocytes, and not monocytes or in vitro derived dendritic cells (DCs), were able to efficiently encode antigen mRNA and expand cognate tumor antigen-specific CD8 T cells ex vivo. Similarly, murine B lymphocytes co-cultured with plasmid DNA, and not DCs, were able to p

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Preclinical and clinical development of DNA vaccines for prostate cancer.

Urologic Oncology Seminars and Original Investigations Elsevier Publications

Dec 2013

Prostate cancer is the most commonly diagnosed cancer in the United States. It is also the second leading cause of cancer-related death in men, making it one of the largest public health concerns today. Prostate cancer is an ideal disease for immunotherapies because of the generally slow progression, the dispensability of the target organ in the patient population, and the availability of several tissue-specific antigens. As such, several therapeutic vaccines have entered clinical trials, with one autologous cellular vaccine (sipuleucel-T) recently gaining Food and Drug Administration approval after demonstrating overall survival benefit in randomized phase III clinical trials. DNA-based vaccines are safe, economical, alternative “off-the-s

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In-silico characterization of ECE-1 inhibitors

Computers in Biology and Medicine Elsevier

Jan 2012

Atherosclerosis is the primary cause of CAD and cerebrovascular disease. Endothelin (ET)-1 is a vasoconstrictive peptide implicated in Atherosclerosis pathology. Endothelin-converting enzyme (ECE) is a membrane metalloprotease that generates endothelin. Reported inhibitors of ECE-1 and their IC50 values were retrieved from literature and their structures were docked with the parent protein using the Molegro virtual docker. The obtained MolDock scores of each of the compounds are hereby reported and are subject to graphical analysis in conjunction with their respective IC50 values to characterize potent inhibitors. A search was then run in the ZINC database for compounds with similar properties. Potent inhibitors with higher Dock scores and

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Phylogenetics and domain analysis of human MAPKs

International Journal of Computational Bioinformatics and In Silico Modeling

Jan 2012

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A Structure Based Drug Design Study on Vegfr-2 Inhibitors

Lambert Academic Publishing Germany

Jan 2011

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A Study on Refractive Errors of a Random Population Selected from Urban Areas of Visakhapatnam, India

International Journal of Engineering Research and Applications

Jan 2011

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