Department of Biotechnology

Indian Institute of Technology Hyderabad (IITH) is a premier institute of science and technology established in 2008. IITH has been consistently ranked in the&nbsp;<a href="https://iith.ac.in/reports/" rel="noopener noreferrer">top 10 institutes</a>&nbsp;in India for Engineering&nbsp;<a href="https://www.nirfindia.org/2021/EngineeringRanking.html" rel="noopener noreferrer" target="_blank">according to NIRF</a>&nbsp;making it one of the most coveted schools for science and technology in the country.

IITH offers&nbsp;<a href="https://iith.ac.in/academics/under-graduate/">undergraduate programs</a>&nbsp;in all the classical engineering disciplines, applied sciences, design, as well as several modern interdisciplinary areas. Students are given a flexibility to explore a broad set of areas, and potentially pursue a minor or double major in a discipline that is not their own. Students who wish to seek a deeper understanding of their own discipline are strongly encouraged to get involved in cutting-edge research with the help of a faculty to mentor them, and earn an Honors in their own field.

The very foundation of IIT Hyderabad is based on&nbsp;<a href="https://iith.ac.in/research/">research and innovation</a>. The vibrant research culture is evident from the number of patents and publications that IITH produces consistently every year. IITH offers&nbsp;<a href="https://iith.ac.in/academics/programmes-offered/">graduate programs</a>&nbsp;at both a masters, and a doctoral level, in several diverse areas. There are separate programs for technology, design, science, and liberal arts. The&nbsp;<a href="https://iith.ac.in/academics/post-graduate/">MTech program</a>&nbsp;is offered in various modes and durations to cater to the ever-growing need of postgraduate level professionals in the country.

IITH encourages and supports&nbsp;<a href="https://iic-iith.netlify.app/index.html" rel="noopener noreferrer" target="_blank">innovation and entrepreneurship</a>&nbsp;at every stage. The minor program in entrepreneurship is open to all students of IITH, and many of the courses are offered by industrialists who are entrepreneurs themselves. There are various&nbsp;<a href="https://iith.ac.in/research/centres-incubators/">innovation centers and incubators</a>&nbsp;that promote entrepreneurship and help mentor young innovators. IITH has been very successful in building tie-ups with leading academic institutions around the globe.

IITH enjoys a very special relationship with Japanese universities and industries that goes beyond academic and research collaborations. In fact, some of the iconic buildings in IITH campus will carry the signature of Japanese architecture.

IITH creates a unique holistic ecosystem for education that offers interactive learning, a very flexible academic structure, cutting-edge research, strong industry collaboration, and entrepreneurship. This is an environment which enables students and faculty to translate their dreams into realities.

IIT Hyderabad

Building on the recent technological advances, all-atom molecular dynamics (MD) simulations have become an indispensable tool to study the molecular behavior at nanoscale. Molecular simulations have been used to characterize the structure, dynamics, and mechanical and electrical properties of DNA origami objects. In this chapter we describe a method to build all-atom model of lipid-spanning DNA origami nanopores and perform molecular dynamics simulations in explicit electrolyte solutions. © 2023, Springer Science+Business Media, LLC, part of Springer Nature.

World University root node

Methods in Molecular Biology

All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores

The essential enzyme CYP121A1 of Mycobacterium tuberculosis forms a functional dimer, which when disrupted results in a decrease of activity and substrate specificity. The crystal structure of CYP121A1 in complex with its substrate di-cyclotyrosine (cYY) indicates that the aromatic side chains of Phe-168 and Trp-182 form stabilizing π-π interactions with a tyrosyl ring of cYY. In the enclosed study, we utilize targeted 19F labeling of aromatic residues to label CYP121A1 for detection by nuclear magnetic resonance (NMR) spectroscopy. 19F-NMR spectra and functional characterization of mutations to Phe-168 and Trp-182 are combined with all-atom molecular dynamics simulations of substrate-bound and substrate-free CYP121A1. This study shows that these aromatic residues interact with cYY predominantly through π-π stacking. In addition to playing an essential role in substrate binding, these active site residues also stabilize the tertiary and quaternary structures of CYP121A1. An additional unexpected finding was the presence of cYY-induced long-range allostery that affects residues located near the homodimer interface. Taken together, this study highlights a structural relationship between the active site environment of this essential enzyme with its global structure that was previously unknown. © 2023 American Chemical Society.

ACS Infectious Diseases

Active Site Aromatic Residues Play a Dual Role in the Substrate Interaction and Protein Structure in Functional Dimers of CYP121A1 of Mycobacterium tuberculosis

The Rauvolfia serpentina strictosidine synthase (RsSTR) enzyme with a bisubstrate activity is central to monoterpenoid indole alkaloid (MIA) biosynthesis pathways, as it stereoselectively condenses the terpenoid and indole metabolites, secologanin and tryptamine, respectively, into strictosidine. Here, cooperativity was aimed to be deciphered by proxy with help of a non-substrate tryptamine analog (decoy compound) to allow a bisubstrate binding without reaction, facilitating an isothermal titration calorimetry (ITC)-based analysis of the effect of the presence of one substrate on the binding of the other. Tryptamine and tryptamine analog bound to RsSTR with similar binding affinities (Kd). On the contrary, ITC revealed an exothermic titration of secologanin to RsSTR but could not fully quantify it because of weak binding. Interestingly, secologanin bound to RsSTR with an apparent binding affinity (Kd,app) of 212.1 μM in the presence of the decoy compound, as opposed to a lack of binding to RsSTR alone, strongly suggesting a “tryptamine-first” mode of binding. Conversely, binding of tryptamine analog in the presence of secologanin was enhanced >3-fold. Further, molecular dynamics simulation (MDS) analyses revealed the conformational flexibility needed for such cooperativity. Our binding studies complemented with the computational analyses suggested cooperativity in the ordered bisubstrate binding to RsSTR. Therefore, understanding thermodynamics and cooperativity in the binding of substrates or ligands would help to unravel the mechanism of enzyme catalysis and ligand-receptor interactions and would guide the redesign of enzymes for enhanced properties and the design of inhibitors against enzymes and receptors. Communicated by Ramaswamy H. Sarma. © 2023 Informa UK Limited, trading as Taylor & Francis Group.

Journal of Biomolecular Structure and Dynamics

Binding order and apparent binding affinity in the bisubstrate activity of strictosidine synthase

Acinetobacter baumannii is an emerging opportunistic pathogen. It exhibits multi-, extreme-, and pan-drug resistance against several classes of antibiotics. Capsular polysaccharide (CPS or K-antigen) is one of the major virulence factors which aids A. baumannii in evading the host immune system. K-antigens of A. baumannii exploit the Wzx/Wzy-dependent pathway that involves 13 different proteins for its assembly and transport onto the outer membrane. A total of 64 (out of 237 K-locus(KL) types) known K-antigen sugar repeating structures are discussed here and are classified into seven groups based on their initial sugars, QuiNAc4NAc, GalNAc, GlcNAc, Gal, QuiNAc/FucNAc, FucNAc, and GlcNAc along with Leg5Ac7Ac/Leg5Ac7R. Thus, the corresponding seven initializing glycosyltransferases (ItrA1, ItrA2, ItrA3, ItrA4, ItrB1, ItrB3, and ItrA3 along with ItrB2) exhibit serotype specificity. The modeled 3D-structural repository of the 64 K-antigens can be accessed at https://project.iith.ac.in/ABSD/k_antigen.html. The topology of K-antigens further reveals the presence of 2-6 and 0-4 sugar monomers in the main and side chains, respectively. The presence of negatively (predominant) or neutrally charged K-antigens is observed in A. baumannii. Such diversity in the K-antigen sugar composition provides the K-typing specificity (viz., 18–69% in terms of reliability) for Wza, Wzb, Wzc, Wzx, and Wzy proteins involved in the Wzx/Wzy-dependent pathway. Interestingly, the degree of uniqueness of these proteins among different K-types is estimated to be 76.79%, considering the 237 reference sequences. This article summarizes the A. baumannii K-antigen structural diversity and creation of a K-antigen digital repository and provides a systematic analysis of the K-antigen assembly and transportation marker proteins. Copyright © 2023 Roshini, Patro, Sundaresan and Rathinavelan.

Fulltext

Frontiers in Microbiology

Structural diversity among Acinetobacter baumannii K-antigens and its implication in the in silico serotyping

The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules. Communicated by Ramaswamy H. Sarma. © 2023 Informa UK Limited, trading as Taylor & Francis Group.

Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study

Kyasanur forest disease (KFD) is a zoonotic disease that is endemic to southern India and caused by KFD virus (KFDV) belonging to the family Flaviviridae. Humans are the dead-end host of the KFDV life cycle. The absence of effective treatment strategies against KFD can be attributed to a lack of studies on the mechanistic part of the spread of the disease. Hypothesizing molecular etiological similarity of KFDV to other well characterized flaviviruses, such as dengue virus (DENV), we focused on predicting the target receptor protein(s) in host and provided molecular basis of receptor-mediated recognition of the human host by KFDV envelop protein (EKFDV), drawing from the extant knowledge on the dengue counterpart, EDENV. Indeed, in silico approach helped to identify that the EKFDV structure closely resembles the EDENV structure and indicated DC-SIGN and/or Mannose receptors to be the plausible target host receptors. Immune-informatics approach aided in predicting 10 epitopes from E, NS1, NS2A, and NS2B proteins of the KFDV-P9605 genotype for vaccine design against KFDV. Further, molecular dynamics simulation (MDS) analyses of their complexes with human leukocyte antigens (HLAs) identified the epitopes DISLTCRVT and YAMEIRPVH as two high ranking candidates for vaccine design. Communicated by Ramaswamy H. Sarma. © 2023 Informa UK Limited, trading as Taylor & Francis Group.

Characterization of host receptor interaction with envelop protein of Kyasanur forest disease virus and predicting suitable epitopes for vaccine candidate

Zinc finger (ZnF) is an important class of nucleic acid and protein recognition domain, wherein, zinc ion is the inorganic co-factor that forms a tetrahedral geometry with the cysteine and/or histidine residues. ZnF domains take up diverse architectures with different ZnF motifs and have a wide range of biological functions. Nonetheless, predicting the ZnF motif(s) from the sequence is quite challenging. To this end, 74 unique ZnF sequence patterns are collected from the literature and classified into 32 different classes. Since the shorter length of ZnF sequence patterns leads to inaccurate predictions, ZnF domain Pfam HMM profiles defined under 6 ZnF Pfam clans (215 HMM profiles) and a few undefined Pfam clans (74 HMM profiles) are used for the prediction. A web server, namely, ZnF-Prot (https://project.iith.ac.in/znprot/) is developed which can predict the presence of 31 ZnF domains in a protein/proteome sequence of any organism. The use of ZnF sequence patterns and Pfam HMM profiles resulted in an accurate prediction of 610 test cases (taken randomly from 249 organisms) considered here. Additionally, the application of ZnF-Prot is demonstrated by considering Arabidopsis thaliana, Homo sapiens, Saccharomyces cerevisiae, Caenorhabditis elegans and Ciona intestinalis proteomes as test cases, wherein, 87–96% of the predicted ZnF motifs are cross-validated. © 2022 Elsevier Ltd

Pattern Recognition

Sequence patterns and HMM profiles to predict proteome wide zinc finger motifs

With the advent of nucleosome/nucleotide intercalating drugs, DNA-based nanocarriers have recently gained impetus. However, most of the newly proposed DNA nanosystems are rather complex, thereby having low scalability and translatability. In this study, we propose a simple DNA nanomatrix core encapsulated within a chitosan shell, which is expected to enhance the encapsulation efficiency of intercalating drugs. This has been demonstrated using proflavine hemisulfate (PfHS), a model intercalating agent that shows improved ROS generation, among other anticancerous properties. The release of the drug from the nanomatrix is triggered by providing a heat trigger using IR-792 perchlorate, a known NIR photothermal sensitizer. © 2023 American Chemical Society.

Department of Biomedical Engineering

ACS Macro Letters

High-Affinity DNA Nanomatrix: A Platform Technology for Synergistic Drug Delivery and Photothermal Therapy

As the manufacturing and development of new synthetic compounds increase to keep pace with the expanding global demand, adverse health effects due to these compounds are emerging as critical public health concerns. Zebrafish have become a prominent model organism to study toxicology due to their genomic similarity to humans, optical clarity, well-defined developmental stages, short generation time, and cost-effective maintenance. It also provides a shorter time frame for in vivo toxicology evaluation compared to the mammalian experimental systems. Here, we used meta-analysis to examine the alteration in genes during cardiotoxicity and neurotoxicity in zebrafish, caused by chemical exposure of any kind. First, we searched the literature comprehensively for genes that are altered during neurotoxicity and cardiotoxicity followed by meta-analysis using ConsensusPathDB. Since constant communication between the heart and the brain is an important physiological phenomenon, we also analyzed interactions among genes altered simultaneously during cardiotoxicity and neurotoxicity using induced network modules analysis in ConsensusPathDB. We observed inflammation and regeneration as the major pathways involved in cardiotoxicity and neurotoxicity. A large number of intermediate genes and input genes anchored in these pathways are molecular regulators of cell cycle progression and cell death and are implicated in tumor manifestation. We propose potential predictive biomarkers for neurotoxicity and cardiotoxicity and the major pathways potentially implicated in the manifestation of a particular toxicity phenotype. © 2023, The Author(s).

Scientific Reports

Interactions between genes altered during cardiotoxicity and neurotoxicity in zebrafish revealed using induced network modules analysis

Leukemia is a heterogeneous group of hematological malignancies distinguished by differentiation blockage and uncontrolled proliferation of myeloid or lymphoid progenitor cells in the bone marrow (BM) and peripheral blood (PB). There are various types of leukemia in which intensive chemotherapy regimens or hematopoietic stem cell transplantation (HSCT) are now the most common treatments associated with severe side effects and multi-drug resistance in leukemia cells. Therefore, it is crucial to develop novel therapeutic approaches with adequate therapeutic efficacy and selectively eliminate leukemic cells to improve the consequences of leukemia. Medicinal plants have been utilized for ages to treat multiple disorders due to their diverse bioactive compounds. Plant-derived products have been used as therapeutic medication to prevent and treat many types of cancer. Over the last two decades, 50 % of all anticancer drugs approved worldwide are from natural products and their derivatives. Therefore this study aims to review natural products such as polyphenols, alkaloids, terpenoids, nitrogen-containing, and organosulfur compounds as antileukemic agents. Current investigations have identified natural products efficiently destroy leukemia cells through diverse mechanisms of action by inhibiting proliferation, reactive oxygen species production, inducing cell cycle arrest, and apoptosis in both in vitro, in vivo, and clinical studies. Current investigations have identified natural products as suitable promising chemotherapeutic and chemopreventive agents. It played an essential role in drug development and emerged as a possible source of biologically active metabolites for therapeutic interventions, especially in leukemia. Data Availability: Data will be made available on request. © 2023 The Authors