Indian Institute of Technology Bombay

About: Indian Institute of Technology Bombay is a education organization based out in Mumbai, India. It is known for research contribution in the topics: Population & Thin film. The organization has 16756 authors who have published 33588 publications receiving 570559 citations.

Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in silico study for drug development.

Abstract: Spike glycoprotein, a class I fusion protein harboring the surface of SARS-CoV-2 (SARS-CoV-2S), plays a seminal role in the viral infection starting from recognition of the host cell surface receptor, attachment to the fusion of the viral envelope with the host cells. Spike glycoprotein engages host Angiotensin-converting enzyme 2 (ACE2) receptors for entry into host cells, where the receptor recognition and attachment of spike glycoprotein to the ACE2 receptors is a prerequisite step and key determinant of the host cell and tissue tropism. Binding of spike glycoprotein to the ACE2 receptor triggers a cascade of structural transitions, including transition from a metastable pre-fusion to a post-fusion form, thereby allowing membrane fusion and internalization of the virus. From ancient times people have relied on naturally occurring substances like phytochemicals to fight against diseases and infection. Among these phytochemicals, flavonoids and non-flavonoids have been the active sources of different anti-microbial agents. We performed molecular docking studies using 10 potential naturally occurring compounds (flavonoids/non-flavonoids) against the SARS-CoV-2 spike protein and compared their affinity with an FDA approved repurposed drug hydroxychloroquine (HCQ). Further, our molecular dynamics (MD) simulation and energy landscape studies with fisetin, quercetin, and kamferol revealed that these molecules bind with the hACE2-S complex with low binding free energy. The study provided an indication that these molecules might have the potential to perturb the binding of hACE2-S complex. In addition, ADME analysis also suggested that these molecules consist of drug-likeness property, which may be further explored as anti-SARS-CoV-2 agents. Communicated by Ramaswamy H. Sarma.

Enhanced topic distillation using text, markup tags, and hyperlinks

Abstract: Topic distillation is the analysis of hyperlink graph structure to identify mutually reinforcing authorities (popular pages) and hubs (comprehensive lists of links to authorities). Topic distillation is becoming common in Web search engines, but the best-known algorithms model the Web graph at a coarse grain, with whole pages as single nodes. Such models may lose vital details in the markup tag structure of the pages, and thus lead to a tightly linked irrelevant subgraph winning over a relatively sparse relevant subgraph, a phenomenon called topic drift or contamination. The problem gets especially severe in the face of increasingly complex pages with navigation panels and advertisement links. We present an enhanced topic distillation algorithm which analyzes text, the markup tag trees that constitute HTML pages, and hyperlinks between pages. It thereby identifies subtrees which have high text- and hyperlink-based coherence w.r.t. the query. These subtrees get preferential treatment in the mutual reinforcement process. Using over 50 queries, 28 from earlier topic distillation work, we analyzed over 700,000 pages and obtained quantitative and anecdotal evidence that the new algorithm reduces topic drift.

Exploring chemical modifications for siRNA therapeutics: a structural and functional outlook.

Abstract: RNA interference (RNAi) is a post-transcriptional gene silencing mechanism induced by small interfering RNAs (siRNAs) and micro-RNAs (miRNAs), and has proved to be one of the most important scientific discoveries made in the last century The robustness of RNAi has opened up new avenues in the development of siRNAs as therapeutic agents against various diseases including cancer and HIV However, there had remained a lack of a clear mechanistic understanding of messenger RNA (mRNA) cleavage mediated by Argonaute2 of the RNA-induced silencing complex (RISC), due to inadequate structural data The X-ray crystal structures of the Argonaute (Ago)-DNA-RNA complexes reported recently have proven to be a breakthrough in this field, and the structural details can provide guidelines for the design of the next generation of siRNA therapeutics To harness siRNAs as therapeutic agents, the prudent use of various chemical modifications is warranted to enhance nuclease resistance, prevent immune activation, decrease off-target effects, and to improve pharmacokinetic and pharmacodynamic properties The focus of this review is to interpret the tolerance of various chemical modifications employed in siRNAs toward RNAi by taking into account the crystal structures and biochemical studies of Ago-RNA complexes Moreover, the challenges and recent progress in imparting druglike properties to siRNAs along with their delivery strategies are discussed

Brimon: a sensor network system for railway bridge monitoring

Abstract: Railway systems are critical in many regions, and can consist of several tens of thousands of bridges, being used over several decades. It is critical to have a system to monitor the health of these bridges and report when and where maintenance operations are needed. This paper presents BriMon, a wireless sensor network based system for such monitoring. The design of BriMon is driven by two important factors: application requirements, and detailed measurement studies of several pieces of the architecture. In comparison with prior bridge monitoring systems and sensor network prototypes, our contributions are three-fold. First, we have designed a novel event detection mechanism that triggers data collection in response to an oncoming train. Next, BriMon employs a simple yet effective multi-channel data transfer mechanism to transfer the collected data onto a sink located on the moving train. Third, the BriMon architecture is designed with careful consideration of the interaction between the multiple requisite functionalities such as time synchronization, event detection, routing, and data transfer. Based on a prototype implementation, this paper also presents several measurement studies to show that our design choices are indeed quite effective.