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Article ; Online: Computational exploration of novel antimicrobial modalities targeting fucose-binding lectins and ribosomes in

Shanthappa, Pallavi M / Suravajhala, Renuka / Kumar, Geetha / Melethadathil, Nidheesh

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–13

Abstract: tRNA-Encoded Peptides (tREPs), encoded by small open reading frames (smORFs) within tRNA genes, have recently emerged as a new class of functional peptides exhibiting antiparasitic activity. The discovery of tREPs has led to a re-evaluation of the role ... ...

Abstract	tRNA-Encoded Peptides (tREPs), encoded by small open reading frames (smORFs) within tRNA genes, have recently emerged as a new class of functional peptides exhibiting antiparasitic activity. The discovery of tREPs has led to a re-evaluation of the role of tRNAs in biology and has expanded our understanding of the genetic code. This presents an immense, unexplored potential in the realm of tRNA-peptide interactions, paving the way for groundbreaking discoveries and innovative applications in various biological functions. This study explores the antimicrobial potential of tREPs against protein targets by employing a computational method that uses verified data sources and highly recognized predictive algorithms to provide a sorted list of likely antimicrobial peptides, which were then filtered for toxicity, cell permeability, allergenicity and half-life. These peptides were then docked with screened protein targets and computationally validated using molecular dynamics (MD) simulations for 150 ns and the binding free energy was estimated. The peptides Pep2 (VVLWRKPRVRKTG) and Pep6 (HRLRLRRRKPWW) exhibited good binding affinities of -110.5 +/- 2.5 and -129.0 +/- 3.9, respectively, with RMSD values of 0.4 and 0.25 nm against the fucose-binding lectin (7NEF) and the 30S ribosome of
Language	English
Publishing date	2024-04-27
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2335555
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Article ; Online: Man vs Microbes - The Race of the Century.

Anderson, Ericka / Nair, Bipin / Nizet, Victor / Kumar, Geetha

Journal of medical microbiology

2023 Volume 72, Issue 1

Abstract: The complexity of the antimicrobial resistance (AMR) crisis and its global impact on healthcare invokes an urgent need to understand the underlying forces and to conceive and implement innovative solutions. Beyond focusing on a traditional pathogen- ... ...

Abstract	The complexity of the antimicrobial resistance (AMR) crisis and its global impact on healthcare invokes an urgent need to understand the underlying forces and to conceive and implement innovative solutions. Beyond focusing on a traditional pathogen-centric approach to antibiotic discovery yielding diminishing returns, future therapeutic interventions can expand to focus more comprehensively on host-pathogen interactions. In this manner, increasing the resiliency of our innate immune system or attenuating the virulence mechanisms of the pathogens can be explored to improve therapeutic outcomes. Key pathogen survival strategies such as tolerance, persistence, aggregation, and biofilm formation can be considered and interrupted to sensitize pathogens for more efficient immune clearance. Understanding the evolution and emergence of so-called 'super clones' that drive AMR spread with rapid clonotyping assays may guide more precise antibiotic regimens. Innovative alternatives to classical antibiotics such as bacteriophage therapy, novel engineered peptide antibiotics, ionophores, nanomedicines, and repurposing drugs from other domains of medicine to boost innate immunity are beginning to be successfully implemented to combat AMR. Policy changes supporting shorter durations of antibiotic treatment, greater antibiotic stewardship, and increased surveillance measures can enhance patient safety and enable implementation of the next generation of targeted prevention and control programmes at a global level.
MeSH term(s)	Humans ; Anti-Bacterial Agents/therapeutic use ; Anti-Bacterial Agents/pharmacology ; Antimicrobial Stewardship ; Drug Tolerance ; Host-Pathogen Interactions
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	218356-0
ISSN	1473-5644 ; 0022-2615
ISSN (online)	1473-5644
ISSN	0022-2615
DOI	10.1099/jmm.0.001646
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Article ; Online: The yield of diabetic retinopathy screening in patients with long-standing diabetes.

Kumar, Geetha / Velu, Saranya / Mathavan, Sinnakaruppan / Raman, Rajiv

Indian journal of ophthalmology

2021 Volume 69, Issue 4, Page(s) 1014–1015

MeSH term(s)	Diabetes Mellitus, Type 2/complications ; Diabetes Mellitus, Type 2/diagnosis ; Diabetic Retinopathy/complications ; Diabetic Retinopathy/diagnosis ; Diabetic Retinopathy/epidemiology ; Glycated Hemoglobin A ; Humans ; Mass Screening
Chemical Substances	Glycated Hemoglobin A
Language	English
Publishing date	2021-01-28
Publishing country	India
Document type	Letter
ZDB-ID	187392-1
ISSN	1998-3689 ; 0301-4738
ISSN (online)	1998-3689
ISSN	0301-4738
DOI	10.4103/ijo.IJO_3721_20
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Article ; Online: Mathematical Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Network with Cytokine Storm, Oxidative Stress, Thrombosis, Insulin Resistance, and Nitric Oxide Pathways.

Sasidharakurup, Hemalatha / Kumar, Geetha / Nair, Bipin / Diwakar, Shyam

Omics : a journal of integrative biology

2021 Volume 25, Issue 12, Page(s) 770–781

Abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a systemic disease affecting not only the lungs but also multiple organ systems. Clinical studies implicate that SARS-CoV-2 infection ... ...

Abstract	Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a systemic disease affecting not only the lungs but also multiple organ systems. Clinical studies implicate that SARS-CoV-2 infection causes imbalance of cellular homeostasis and immune response that trigger cytokine storm, oxidative stress, thrombosis, and insulin resistance. Mathematical modeling can offer in-depth understanding of the SARS-CoV-2 infection and illuminate how subcellular mechanisms and feedback loops underpin disease progression and multiorgan failure. We report here a mathematical model of SARS-CoV-2 infection pathway network with cytokine storm, oxidative stress, thrombosis, insulin resistance, and nitric oxide (NO) pathways. The biochemical systems theory model shows autocrine loops with positive feedback enabling excessive immune response, cytokines, transcription factors, and interferons, which can imbalance homeostasis of the system. The simulations suggest that changes in immune response led to uncontrolled release of cytokines and chemokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor α (TNFα), and affect insulin, coagulation, and NO signaling pathways. Increased production of NETs (neutrophil extracellular traps), thrombin, PAI-1 (plasminogen activator inhibitor-1), and other procoagulant factors led to thrombosis. By analyzing complex biochemical reactions, this model forecasts the key intermediates, potential biomarkers, and risk factors at different stages of COVID-19. These insights can be useful for drug discovery and development, as well as precision treatment of multiorgan implications of COVID-19 as seen in systems medicine.
MeSH term(s)	COVID-19/immunology ; COVID-19/virology ; Cytokine Release Syndrome/immunology ; Cytokine Release Syndrome/virology ; Cytokines/immunology ; Humans ; Insulin Resistance/immunology ; Models, Theoretical ; Nitric Oxide/immunology ; Oxidative Stress/immunology ; SARS-CoV-2/immunology ; Signal Transduction/immunology ; Thrombosis/immunology ; Thrombosis/virology
Chemical Substances	Cytokines ; Nitric Oxide (31C4KY9ESH)
Language	English
Publishing date	2021-11-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2030312-9
ISSN	1557-8100 ; 1536-2310
ISSN (online)	1557-8100
ISSN	1536-2310
DOI	10.1089/omi.2021.0155
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Article ; Online: Compliance with follow-up in patients with diabetic macular edema: Eye care center vs. diabetes care center.

Kumar, Geetha / Velu, Saranya / Rajalakshmi, Ramachandran / Surya, Janani / Mohan, Viswanathan / Raman, Aayushi / Raman, Rajiv

Indian journal of ophthalmology

2023 Volume 71, Issue 6, Page(s) 2531–2536

Abstract: Purpose: The study was conducted to compare the compliance to intravitreal injection treatment and follow-up in patients with center-involving diabetic macular edema (CI-DME) and treatment outcomes between a tertiary eye care facility and a tertiary ... ...

Abstract	Purpose: The study was conducted to compare the compliance to intravitreal injection treatment and follow-up in patients with center-involving diabetic macular edema (CI-DME) and treatment outcomes between a tertiary eye care facility and a tertiary diabetes care center. Methods: A retrospective review was conducted on treatment naïve DME patients who had received intravitreal anti-vascular endothelial growth factor (anti-VEGF) injections in 2019. Participants were people with type 2 diabetes who were under regular care at the eye care center or the diabetes care center in Chennai. The outcome measures were noted at months 1, 2, 3, 6, and 12. Results: A review of 136 patients treated for CI-DME (72 from the eye care center and 64 from a diabetes care center) was carried out. The severity of diabetic retinopathy (DR) was similar in both centers. There was no statistically significant (P > 0.05) difference in the choice of initial intravitreal drug in the two centers. At 12-month follow-up, only 29.16% came for a follow-up in the eye center vs. 76.56% in a diabetes care center (P = 0.000). The multivariate logistic regression showed increasing age was associated with non-compliance in both the groups (eye care center: odds ratio [OR] 0.91; 95% confidence interval [CI] 0.82-1.21; P = 0.044) and diabetes care center (OR 1.15; 95% CI 1.02-1.29; P = 0.020). Conclusion: The follow-up rate between eye care and diabetic care center with DME showed a significant disparity. By providing comprehensive diabetes care for all complications under one roof, compliance with follow-up can be improved in people with DME.
MeSH term(s)	Humans ; Angiogenesis Inhibitors ; Diabetes Mellitus, Type 2/complications ; Diabetes Mellitus, Type 2/epidemiology ; Diabetic Retinopathy/complications ; Diabetic Retinopathy/diagnosis ; Diabetic Retinopathy/drug therapy ; Follow-Up Studies ; India/epidemiology ; Macular Edema/diagnosis ; Macular Edema/drug therapy ; Macular Edema/etiology ; Ranibizumab ; Vascular Endothelial Growth Factor A
Chemical Substances	Angiogenesis Inhibitors ; Ranibizumab (ZL1R02VT79) ; Vascular Endothelial Growth Factor A
Language	English
Publishing date	2023-06-15
Publishing country	India
Document type	Journal Article
ZDB-ID	187392-1
ISSN	1998-3689 ; 0301-4738
ISSN (online)	1998-3689
ISSN	0301-4738
DOI	10.4103/IJO.IJO_220_23
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Article ; Online: Systematic understanding of anti-tumor mechanisms of Tamarixetin through network and experimental analyses.

Shaji, Sanu K / Drishya, G / Sunilkumar, Damu / Suravajhala, Prashanth / Kumar, Geetha B / Nair, Bipin G

Scientific reports

2022 Volume 12, Issue 1, Page(s) 3966

Abstract: Tamarixetin, a flavonoid derived from Quercetin, was shown to possess anti-cancer properties in various types of cancer. However, the mechanism of action of this compound is not well understood. Observations from reverse docking and network pharmacology ... ...

Abstract	Tamarixetin, a flavonoid derived from Quercetin, was shown to possess anti-cancer properties in various types of cancer. However, the mechanism of action of this compound is not well understood. Observations from reverse docking and network pharmacology analysis, were validated by cell based studies to analyse the chemotherapeutic potential and elucidate the molecular mechanism of action of Tamarixetin in breast cancer. In silico analysis using reverse docking and PPI analysis clearly indicated that out of 35 proteins targeted by Tamarixetin, the top 3 hub genes, namely, AKT1, ESR1 and HSP90AA1, were upregulated in breast tumor tissues and more importantly showed strong negative correlation to breast cancer patient survival. Furthermore, the KEGG pathway analysis showed enrichment of target proteins of Tamarixetin in 33 pathways which are mainly involved in neoplastic signalling. In vitro cell-based studies demonstrated that Tamarixetin could inhibit cell proliferation, induce ROS and reduce mitochondrial membrane potential, leading to cell death. Tamarixetin induced cell cycle arrest at G2/M phase and inhibited the migration as well as the invasion of breast cancer cells. Taken together, the combination of in silico and in vitro approaches used in the present study clearly provides evidence for the chemotherapeutic potential of Tamarixetin in breast cancer.
MeSH term(s)	Breast Neoplasms/drug therapy ; Disaccharides/pharmacology ; Drugs, Chinese Herbal/pharmacology ; Female ; Humans ; Molecular Docking Simulation ; Quercetin/analogs & derivatives ; Quercetin/pharmacology ; Quercetin/therapeutic use
Chemical Substances	Disaccharides ; Drugs, Chinese Herbal ; tamarixetin (73WRA8Z8M8) ; Quercetin (9IKM0I5T1E)
Language	English
Publishing date	2022-03-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-07087-6
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Article ; Online: In silico

Shanthappa, Pallavi M / Suravajhala, Renuka / Suravajhala, Prashanth / Kumar, Geetha / Melethadathil, Nidheesh

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 12, Page(s) 5696–5706

Abstract: Norovirus (NoV) belongs to the Calciviridae family that causes diarrhoea, vomiting, and stomach pain in people who have acute gastroenteritis (AGE). Identifying multi-epitope dependent vaccines for single stranded positive sense viruses such as NoV has ... ...

Abstract	Norovirus (NoV) belongs to the Calciviridae family that causes diarrhoea, vomiting, and stomach pain in people who have acute gastroenteritis (AGE). Identifying multi-epitope dependent vaccines for single stranded positive sense viruses such as NoV has been a long due. Although efforts have been in place to look into the candidate epitopes, understanding molecular mimicry and finding new epitopes for inducing immune responses against the T/B-cells which play an important role for the cell-mediated and humoral immunity was not dealt with in great detail. The current study focuses on identifying new epitopes from various databases that were filtered for antigenicity, allergenicity, and toxicity. The adjuvant β-defensin along with different linkers were used for vaccine construction. Further, the binding relationship between the vaccine construct and toll-like immune receptor (TLR3) complex was determined using a molecular docking analysis, followed by molecular dynamics simulation of 100 ns. The vaccine candidate developed expresses good solubility with a score of 0.530,
MeSH term(s)	Humans ; Molecular Docking Simulation ; Epitopes, T-Lymphocyte ; Norovirus/metabolism ; Epitopes, B-Lymphocyte ; Toll-Like Receptor 3 ; Vaccines, Subunit ; Computational Biology
Chemical Substances	Epitopes, T-Lymphocyte ; Epitopes, B-Lymphocyte ; Toll-Like Receptor 3 ; Vaccines, Subunit
Language	English
Publishing date	2022-08-02
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2105400
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Article ; Online: Patient, family member, and health care provider perspective on barriers and facilitators to diabetic retinopathy screening in Thailand: A qualitative study.

Kumar, Geetha / Velu, Saranya / Pardhan, Shahina / Sapkota, Raju / Ruamviboonsuk, Paisan / Tadarati, Mongkol / Chotcomwongse, Peranut / Nganthavee, Variya / Pattanapongpaiboon, Warisara / Raman, Rajiv

PloS one

2023 Volume 18, Issue 8, Page(s) e0289618

Abstract: Objectives: Diabetic retinopathy (DR) can cause significant visual impairment which can be largely avoided by early detection through proper screening and treatment. People with DR face a number of challenges from early detection to treatment. The aim ... ...

Abstract	Objectives: Diabetic retinopathy (DR) can cause significant visual impairment which can be largely avoided by early detection through proper screening and treatment. People with DR face a number of challenges from early detection to treatment. The aim of this study was to investigate factors that influence DR screening in Thailand and to identify barriers to follow-up compliance from patient, family member, and health care provider (HCP) perspectives. Methods: A total of 15 focus group discussions (FGDs) were held, each with five to twelve participants. There were three distinct stakeholders: diabetic patients (n = 47) presenting to a diabetic retinopathy clinic in Thailand, their family members (n = 41), and health care providers (n = 34). All focus group conversations were transcribed verbatim. Thematic analysis was used to examine textual material. Results: Different themes emerged from the FGD on knowledge about diabetes, self-care behaviors of diabetes mellitus (DM), awareness about DR, barriers to DR screening, and the suggested solutions to address those barriers. Data showed lower knowledge and awareness about diabetes and DR in both patients and family members. Long waiting times, financial issues, and lack of a person to accompany appointments were identified as the major deterrents for attending DR screening. Family support for patients was found to vary widely, with some patients reporting to have received adequate support while others reported having received minimal support. Even though insurance covered the cost of attending diabetes/DR screening program, some patients did not show up for their appointments. Conclusion: Patients need to be well-informed about the asymptomatic nature of diabetes and DR. Communication at the patient level and shared decision-making with HCPs are essential. Family members and non-physician clinicians (such as diabetes nurses, diabetes educators, physician assistants) who work in the field of diabetes play a vital role in encouraging patients to attend diabetes and DR follow-ups visits regularly.
MeSH term(s)	Humans ; Diabetic Retinopathy/diagnosis ; Diabetic Retinopathy/etiology ; Thailand ; Patient Compliance ; Mass Screening/adverse effects ; Health Personnel ; Family ; Diabetes Mellitus/diagnosis
Language	English
Publishing date	2023-08-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0289618
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Article ; Online: Comparative molecular profiling of multidrug-resistant

Menon, Nitasha D / Somanath, Priyanka / Jossart, Jennifer / Vijayakumar, Gayathri / Shetty, Kavya / Baswe, Manasi / Chatterjee, Meghna / Hari, Malavika B / Nair, Samitha / Kumar, V Anil / Nair, Bipin G / Nizet, Victor / Perry, J Jefferson P / Kumar, Geetha B

JAC-antimicrobial resistance

2024 Volume 6, Issue 1, Page(s) dlae001

Abstract: Objectives: We sought to analyse the antibiotic susceptibility profiles and molecular epidemiology of MDR clinical : Methods: We established a comprehensive clinical strain library consisting of 58 isolates collected from patients across the South ... ...

Abstract	Objectives: We sought to analyse the antibiotic susceptibility profiles and molecular epidemiology of MDR clinical Methods: We established a comprehensive clinical strain library consisting of 58 isolates collected from patients across the South Indian state of Kerala from March 2017 to July 2019. The strains were subject to antibiotic susceptibility testing, modified carbapenem inactivation method assay for carbapenemase production, PCR sequencing, comparative sequence analysis and quantitative PCR of MDR determinants associated with antibiotic efflux pump systems, fluoroquinolone resistance and carbapenem resistance. We performed Results: Of our collection of South Indian Conclusions: This study provides insight into MDR mechanisms adopted by
Language	English
Publishing date	2024-01-16
Publishing country	England
Document type	Journal Article
ISSN	2632-1823
ISSN (online)	2632-1823
DOI	10.1093/jacamr/dlae001
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Article ; Online: Independent component analysis reveals 49 independently modulated gene sets within the global transcriptional regulatory architecture of multidrug-resistant

Menon, Nitasha D / Poudel, Saugat / Sastry, Anand V / Rychel, Kevin / Szubin, Richard / Dillon, Nicholas / Tsunemoto, Hannah / Hirose, Yujiro / Nair, Bipin G / Kumar, Geetha B / Palsson, Bernhard O / Nizet, Victor

mSystems

2024 Volume 9, Issue 2, Page(s) e0060623

Abstract: Acinetobacter ... ...

Abstract	Acinetobacter baumannii
MeSH term(s)	Humans ; Acinetobacter baumannii/genetics ; Acinetobacter Infections/drug therapy ; Virulence/genetics ; Gene Expression Regulation ; Anti-Bacterial Agents/pharmacology
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00606-23
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