Publications by authors named "Krupanidhi Srirama"

10 Publications

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Insilico drug repurposing using FDA approved drugs against Membrane protein of SARS-CoV-2.

J Pharm Sci 2021 Mar 5. Epub 2021 Mar 5.

Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, 522213, Andhra Pradesh, India. Electronic address:

The novel coronavirus (SARS-CoV-2) outbreak has started taking away the millions of lives worldwide. Identification of known and approved drugs against novel coronavirus disease (COVID-19) seems to be an urgent need for the repurposing of the existing drugs. So, here we examined a safe strategy of using approved drugs of SuperDRUG2 database against modeled membrane protein (M-protein) of SARS-CoV-2 which is essential for virus assembly by using molecular docking-based virtual screening. A total of 3639 drugs from SuperDRUG2 database and additionally 14 potential drugs reported against COVID-19 proteins were selected. Molecular docking analyses revealed that nine drugs can bind the active site of M-protein with desirable molecular interactions. We therefore applied molecular dynamics simulations and binding free energy calculation using MM-PBSA to analyze the stability of the compounds. The complexes of M-protein with the selected drugs were simulated for 50 ns and ranked according to their binding free energies. The binding mode of the drugs with M-protein was analyzed and it was observed that Colchicine, Remdesivir, Bafilomycin A1 from COVID-19 suggested drugs and Temozolomide from SuperDRUG2 database displayed desirable molecular interactions and higher binding affinity towards M-protein. Interestingly, Colchicine was found as the top most binder among tested drugs against M-protein. We therefore additionally identified four Colchicine derivatives which can bind efficiently with M-protein and have better pharmacokinetic properties. We recommend that these drugs can be tested further through in vitro studies against SARS-CoV-2 M-protein.
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http://dx.doi.org/10.1016/j.xphs.2021.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934671PMC
March 2021

Design of a multi-epitope-based vaccine targeting M-protein of SARS-CoV2: an immunoinformatics approach.

J Biomol Struct Dyn 2020 Nov 30:1-15. Epub 2020 Nov 30.

Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India.

In the present study, one of the targets present on the envelopes of coronaviruses, membrane glycoprotein (M) was chosen for the design of a multi-epitope vaccine by Immunoinformatics approach. The B-cell and T-cell epitopes used for the construction of vaccine were antigenic, nonallergic and nontoxic. An adjuvant, β-defensin and PADRE sequence were included at the N-terminal end of the vaccine. All the epitopes were joined by linkers for decreasing the junctional immunogenicity. Various physicochemical parameters of the vaccine were evaluated. Secondary and tertiary structures were predicted for the vaccine construct. The tertiary structure was further refined, and various parameters related to the refinement of the protein structure were validated by using different tools. Humoral immunity induced by B-cells relies upon the identification of antigenic determinants on the surface of the vaccine construct. In this regard, the vaccine construct was found to consist of several B-cell epitopes in its three-dimensional conformation. Molecular docking of the vaccine was carried out with TLR-3 receptor to study their binding and its strength. Further, protein-protein interactions in the docked complex were visualized using LigPlot+. Population coverage analysis had shown that the multi-epitope vaccine covers 94.06% of the global population. The vaccine construct was successfully cloned into pET-28a (+). Immune simulation studies showed the induction of primary, secondary and tertiary immune responses marked by the increased levels of antibodies, INF-γ, IL-2, TGF-β, B- cells, CD4+ and CD8+ cells. Finally, the vaccine construct was able to elicit immune response as desired. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1850357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7754933PMC
November 2020

Screening of Leaf Extract for Identification of Bioactive Compounds and Evaluation of Its Antiproliferative Activity Against MCF-7 and HeLa Cells.

Food Technol Biotechnol 2020 Mar;58(1):71-75

Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research (Deemed to be University), Vadlamudi-522213, Guntur, Andhra Pradesh, India.

Mangroves contain a wide range of bioactive compounds with pharmacological activities. In the present study, we analysed the separation and detection of phytoconstituents with the methanol extract of leaf using gas chromatography-mass spectrometry (GC-MS) and tested its cytotoxicity effect against MCF-7 and HeLa cells. Phytochemical compounds such as docosanoic, octadecatrienoic and -9-octadecanoic acids, triterpenoid γ-sitosterol, and terpene alcohol in methanol extract of leaf were identified. Furthermore, antiproliferative activity of the extract of leaf was evaluated using MCF-7 and HeLa cells. The results indicated a reduction of cell viability of 37.43 and 41.89% of MCF-7 and HeLa cells respectively. The methanol extract of leaf proved to be effective in protecting the cells against oxidative stress. This is the first report on the cytotoxicity effect of leaf extract on MCF-7 and HeLa cells.
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http://dx.doi.org/10.17113/ftb.58.01.20.6351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7365333PMC
March 2020

Huntington's chorea, a neurological disorder of all ages - Bioinformatics approach for its precise diagnosis.

Int J Health Sci (Qassim) 2019 Nov-Dec;13(6):26-30

Department of Biotechnology, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Andhra Pradesh, India.

Background: The disease that obstructs social movements of people is Huntington's disease (HD). Hence, the expedition of its molecular aspects and bioinformatics tools relating to precise confirmation of the disease is warranted. Due to social stigma, the care and attention to safeguard these patients had increased at community level.

Objective: The objective of the study was to explore bioinformatics tools to trace the defects in Huntington's gene and design its small-guided RNA (sgRNA).

Methodology: The HTT gene sequence was retrieved, CRISPR sites were identified, and gRNA sequence was determined using the University of California Santa Cruz (UCSC) Genome Browser. HTT protein molecular structure elucidation was retrieved through PDB and Swiss Model. Ramachandran plot displayed the cluster of poly-Q at the Phi (-60--36) and Psi (-60--65) regions. The pattern of residues in the plot displayed that the HTT protein is alpha-helical predominant.

Results: The CRISPR sites on HTT gene are viewed and sgRNA sequences are obtained through the UCSC Genome Browser. This sgRNA sequence along with Cas9 would be planned for genome editing in future experimental models. The Ramachandran plot for HTT protein derived through online Rampage revealed the recurrent appearance of polyglutamine (Q) at the Phi (-55--65) and Psi (120-135) regions.

Conclusion: Online bioinformatic tools such as UCSC Genome Browser, Swiss-Model, and Rampage help in exploring molecular basis of HD and disease-causing protein HTT, and the same invariably assists in creating awareness among health workers.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6852502PMC
November 2019

In silico sgRNA tool design for CRISPR control of quorum sensing in species.

Genes Dis 2018 Jun 11;5(2):123-129. Epub 2018 Apr 11.

Department of Biotechnology, Vikrama Simhapuri University, Nellore, India.

CRISPR genome editing utilizes Cas9 nuclease and single guide RNA (sgRNA), which directs the nuclease to a specific site in the genome and makes a double-stranded break (DSB). Design of sgRNA for CRISPR-Cas targeting, and to promote CRISPR adaptation, uses a regulatory mechanism that ensures maximum CRISPR-Cas9 system functions when a bacterial population is at highest risk of phage infection. is the most regularly identified gram-negative bacterium infecting patients. Recent reports have demonstrated that the extent of diseases caused by is expanding and, in a few cases, now surpasses the quantity of infections caused by . Most strains possess biofilm-forming ability, which plays a major role in virulence and drug resistance. Biofilm bacteria use quorum sensing, a cell-to-cell communication process, to activate gene expression. Many genes are involved in biofilm formation and the mechanism to disrupt the biofilm network is still not clearly understood. In this study, we performed in silico gene editing to exploit the gene, responsible for biofilm formation. The study explored different tools available for genome editing to create gene knockouts, selecting the gene as a target.
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http://dx.doi.org/10.1016/j.gendis.2018.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146548PMC
June 2018

Recent Advances in Probiotics as Live Biotherapeutics Against Gastrointestinal Diseases.

Curr Pharm Des 2018 ;24(27):3162-3171

Department of Biotechnology, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Guntur-522213, Andhra Pradesh, India.

Background: Gastrointestinal (GI) diseases are a major cause of emergency department visits requiring hospitalizations leading to considerable burden on global economy. Several factors contribute to the onset of gastrointestinal diseases such as pathogens (parasites, bacteria, virus, toxins etc.), autoimmune disorders and severe inflammation of intestine.

Objective: One common feature among all these diseases is the dysentery and alteration of gut microbiota composition (gut dysbiosis). Apart from conventional therapies such as antibiotics and ORS supplementation, gut microbiota modulation with probiotic supplementation has emerged as a successful and healthy alternative in mitigating GI diseases. In this review our goal is to discuss the causes of gastrointestinal diseases and the present state of various therapeutic strategies such as probiotics as live biotherapeutics and Fecal Microbial Transplants (FMT's).

Conclusion: Several reports and clinical trials point out to the beneficial effects of probiotics in modulating the gut microbiota and improving the side effects of gastrointestinal diseases. Live biotherapeutics and FMT's could be suitable and successful alternatives to conventional therapies in mitigating the gastrointestinal pathogens.
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http://dx.doi.org/10.2174/1381612824666180717105128DOI Listing
November 2019

An efficient method for integration of PCR fragments into adjacent or overlapping restriction sites during gene cloning.

3 Biotech 2018 Apr 24;8(4):197. Epub 2018 Mar 24.

Department of Biotechnology, Vignan's Foundation for Science, Technology and Research (VFSTR), Vadlamudi, Guntur District, Andhra Pradesh 522213 India.

In the present work, a simple and straightforward method was developed to clone any PCR-amplified products into restriction sites that are very close, adjacent or overlapping in the expression vector. The novelty of the methodology involves a crucial primer-designing step by adding appropriate overhangs to the 5' ends of primers based on the multiple cloning sites (MCS) (polylinker) region of expression vector. After PCR amplification, actual cloning is performed not in adjacent RE sites, but in sites that are little distant in the MCS. However, the sites lost during this cloning step are maintained intact since they are provided by the cloned PCR product (through the primer overhangs). Gene for green fluorescent protein (GFP) was cloned and expressed employing this strategy to demonstrate its simplicity. This method is highly useful for vector modification without losing the restriction sites present in the MCS.
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http://dx.doi.org/10.1007/s13205-018-1214-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5866252PMC
April 2018

An Update on Clinical Burden, Diagnostic Tools, and Therapeutic Options of .

Infect Dis (Auckl) 2017 22;10:1179916117703999. Epub 2017 May 22.

Department of Biotechnology, Vignan's University, Guntur, India.

is an important pathogen responsible for a variety of diseases ranging from mild skin and soft tissue infections, food poisoning to highly serious diseases such as osteomyelitis, endocarditis, and toxic shock syndrome. Proper diagnosis of pathogen and virulence factors is important for providing timely intervention in the therapy. Owing to the invasive nature of infections and the limited treatment options due to rampant spread of antibiotic-resistant strains, the trend for development of vaccines and antibody therapy is increasing at rapid rate than development of new antibiotics. In this article, we have discussed elaborately about the host-pathogen interactions, clinical burden due to infections, status of diagnostic tools, and treatment options in terms of prophylaxis and therapy.
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http://dx.doi.org/10.1177/1179916117703999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443039PMC
May 2017

IMMUNOLOGICAL IMPLICATIONS IN MAMMALIAN SEMI-ALLOGENEIC PREGNANCY.

Roum Arch Microbiol Immunol 2015 Jul-Dec;74(3-4):99-104

The mammalian conceptus is a semi-allograft. The maternal tolerance towards semi-allograft is primed by a battery of cytokines and resident decidual cells. Invasion of embryonic trophoblast, decidual vascular remodeling and unresponsive incipient 'Triple-negative' (CD3-, CD4- and CD8-) T-cells of foetus promote normal pregnancy. On the other hand, the maternal cytokine profile shift towards Th1 response is shown to enhance the risk during pregnancy. The periodical examination of maternal serum levels of Th1 and Th2 response mediated cytokines constitutes prognostic biomarkers to initiate therapeutic regimens.
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July 2016

Omega-3 fatty acids for nutrition and medicine: considering microalgae oil as a vegetarian source of EPA and DHA.

Curr Diabetes Rev 2007 Aug;3(3):198-203

Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Nilayam, India.

Long-chain EPA/DHA omega-3 fatty acid supplementation can be co-preventative and co-therapeutic. Current research suggests increasing accumulated long chain omega-3s for health benefits and as natural medicine in several major diseases. But many believe plant omega-3 sources are nutritionally and therapeutically equivalent to the EPA/DHA omega-3 in fish oil. Although healthy, precursor ALA bio-conversion to EPA is inefficient and production of DHA is nearly absent, limiting the protective value of ALA supplementation from flax-oil, for example. Along with pollutants certain fish acquire high levels of EPA/DHA as predatory species. However, the origin of EPA/DHA in aquatic ecosystems is algae. Certain microalgae produce high levels of EPA or DHA. Now, organically produced DHA-rich microalgae oil is available. Clinical trials with DHA-rich oil indicate comparable efficacies to fish oil for protection from cardiovascular risk factors by lowering plasma triglycerides and oxidative stress. This review discusses 1) omega-3 fatty acids in nutrition and medicine; 2) omega-3s in physiology and gene regulation; 3) possible protective mechanisms of EPA/DHA in major diseases such as coronary heart disease, atherosclerosis, cancer and type 2 diabetes; 4) EPA and DHA requirements considering fish oil safety; and 5) microalgae EPA and DHA-rich oils and recent clinical results.
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http://dx.doi.org/10.2174/157339907781368968DOI Listing
August 2007