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Yasmin S, Ansari MY, Pandey K, Dikhit MR. Identification of potential vaccine targets for elicitation of host immune cells against SARS-CoV-2 by reverse vaccinology approach. Int J Biol Macromol 2024; 265:130754. [PMID: 38508555 DOI: 10.1016/j.ijbiomac.2024.130754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
The COVID-19 pandemic has emerged as a critical global health crisis, demanding urgent and effective strategies for containment. While some knowledge exists about epitope sequences recognized by human immune cells and their activation of CD8+ T cells within the HLA context, comprehensive information remains limited. This study employs reverse vaccinology to explore antigenic HLA-restricted T-cell epitopes capable of eliciting durable immunity. Screening reveals 187 consensus epitopes, with 23 offering broad population coverage worldwide, spanning over 5000 HLA alleles. Sequence alignment analysis highlights the genetic distinctiveness of these peptides from Homo sapiens and their intermediate to high TAP binding efficiency. Notably, these epitopes share 100 % sequence identity across strains from nine countries, indicating potential for a uniform protective immune response among diverse ethnic populations. Docking simulations further confirm their binding capacity with the HLA allele, validating them as promising targets for SARS-CoV-2 immune recognition. The anticipated epitopes are connected with suitable linkers and adjuvant, and then assessed for its translational efficacy within a bacterial expression vector through computational cloning. Through docking, it is observed that the chimeric vaccine construct forms lasting hydrogen bonds with Toll-like receptor (TLR4), while immune simulation illustrates an increased cytotoxic response aimed at CD8+ T cells. This comprehensive computational analysis suggests the chimeric vaccine construct's potential to provoke a robust immune response against SARS-CoV-2. By delineating these antigenic fragments, our study offers valuable insights into effective vaccine and immunotherapy development against COVID-19, contributing significantly to global efforts in combating this infectious threat.
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Affiliation(s)
- Sabina Yasmin
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University (KKU), Abha 62529, Saudi Arabia
| | - Mohammad Yousuf Ansari
- Department of Pharmaceutical Chemistry, M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, India.
| | - Krishna Pandey
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India
| | - Manas Ranjan Dikhit
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna 800007, India.
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2
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Dikhit MR, Sen A. Elucidation of conserved multi-epitope vaccine against Leishmania donovani using reverse vaccinology. J Biomol Struct Dyn 2024; 42:1293-1306. [PMID: 37054523 DOI: 10.1080/07391102.2023.2201630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/29/2023] [Indexed: 04/15/2023]
Abstract
Visceral leishmaniasis (VL) is a tropical disease that causes severe public health problems in humans when untreated. As no licensed vaccine exists against VL, we aimed to formulate a potential MHC-restricted chimeric vaccine construct against this dreadful parasitic disease. Amastin-like protein derived from L. donovani is considered to be stable, immunogenic and non-allergic. A comprehensive established framework was used to explore the set of immunogenic epitopes with estimated population coverage of 96.08% worldwide. The rigorous assessment revealed 6 promiscuous T-epitopes which can plausibly be presented by more than 66 diverse HLA alleles. Further docking and simulation study of peptide receptor complexes identified a strong and stable binding interaction with better structural compactness. The predicted epitopes were combined with appropriate linkers and adjuvant molecules and their translation efficiency was evaluated in pET28+(a), an bacterial expression vector using in-silico cloning. Molecular docking followed by MD simulation study revealed a stable interaction between chimeric vaccine construct with TLRs. Immune simulation of the chimeric vaccine constructs showed an elevated Th1 immune response against both B and T epitopes. With this, the detailed computational analysis suggested that the chimeric vaccine construct can evoke a robust immune response against Leishmania donovani infection. Future studies are required to validate the role of amastin as a promising vaccine target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manas Ranjan Dikhit
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Abhik Sen
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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3
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Singh S, Madhukar M, Dikhit MR, Ravidas VN, Pandey K, Sen A. Transcriptome analysis of dermal fibroblasts derived from VL and PKDL patients reveal disease specific gene expression and pathological regulation. J Infect Dis 2023; 227:1132-1142. [PMID: 36821723 DOI: 10.1093/infdis/jiad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/28/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Post kala-azar dermal leishmaniasis (PKDL), a dermal form of the disease, occurs in some of the visceral leishmaniasis (VL) patients following treatment. The PKDL disease mechanism is yet not clearly understood. OBJECTIVES Here we have studied the role of dermal fibroblasts in VL and PKDL disease mechanism. METHODS Dermal fibroblasts were grown from skin biopsy explants collected from individual VL & PKDL patients and healthy controls. Fibroblasts from third passage were subjected to RNA-Seq for analyzing differentially-expressed genes (DEGs). Significantly important genes were further validated by RT-PCR and ELISA. RESULTS Transcriptome analysis of PKDL vs VL identified 516 DEGs (263 were overrepresented and 253 were underrepresented in PKDL). Among the top Hub-genes, MMP2, IL1β, CXCL8, IFIH1, NFKB1A, IL6, ISG15 and EGFR were underexpressed and ACTB, HSP90AA1, RAB7A and RPS27A were overexpressed in PKDL compared to VL. CONCLUSIONS Our data indicates that PKDL fibroblasts may present antigens through MHC I pathway activating CD8+ T-cell mediated response while the VL fibroblasts express NFκB mediated chemokines, IL1β, IL6 and IL8 resulting in the recruitment of NK-cells and monocytes to the site of infection leading to the clearance of parasite from the skin and visceralization of the disease.
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Affiliation(s)
- Sneha Singh
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Major Madhukar
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Manas Ranjan Dikhit
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Vidya Nand Ravidas
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Krishna Pandey
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Abhik Sen
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
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Abhishek K, Kumar A, Sardar AH, Vijayakumar S, Dikhit MR, Kumar A, Kumar V, Das S, Das P. Differential translational regulation of host exosomal proteins play key role in immunomodulation in antimony resistance in Visceral Leishmaniasis: A proteomic profiling study. Acta Trop 2022; 226:106268. [PMID: 34890541 DOI: 10.1016/j.actatropica.2021.106268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 10/25/2021] [Accepted: 12/05/2021] [Indexed: 11/01/2022]
Abstract
In host-pathogen interactions, exosomal secretions are crucial for cell to cell communication and have an established role in immunomodulation. Protozoans, including Leishmania, modulates their host vesicular secretions for better survival; although the role of exosomal secretions in unresponsive against sodium antimony gluconate (SAG) has never been documented. In this study, the exosomal proteome of RAW macrophages infected with either SAG responsive (SAGS) or SAG unresponsive (SAGR) L. donovani parasites has been compared with uninfected RAW macrophages. Proteins isolated from exosomes were labelled with iTRAQ reagents; followed by subsequent LC-TOF/-MS analysis. In total, 394 proteins (p < 0.05) were identified which were shared common among all sets. Highly differentially expressed proteins were sorted by log2 value -1 and +1 as down regulated and up regulated respectively which yielded 58 proteins in SAGR and 41 proteins during SAGS infection. Out of the 58 proteins identified during SAGR infection, 17 proteins were of immune modulatory function. Network visualization model and pathway analysis revealed the interactions among these proteins via different immunological pathways with reported involvement of some proteins in SAG resistance and host immune modulation. Hence, the differential abundance of immune pathway related proteins in exosomes of infected host during SAGR infection supports the immune modulatory strategy adopted by SAG resistant parasites for enhanced survival .
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Praharaj I, Jain A, Singh M, Balakrishnan A, Dhodapkar R, Borkakoty B, Ashok M, Das PD, Biswas D, Kalawat U, Turuk J, Sugunan AP, Prakash S, Singh AK, Barathidasan R, Subhadra S, Sabat J, Manjunath MJ, Kanta P, Mudhigeti N, Hazarika R, Mishra H, Abhishek K, Santhalembi C, Dikhit MR, Vijay N, Narayan J, Kaur H, Giri S, Gupta N. Authors' response. Indian J Med Res 2021; 153:563. [PMID: 34643564 PMCID: PMC8555583 DOI: 10.4103/0971-5916.318161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Ira Praharaj
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Mini Singh
- Department of Virology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | | | - Rahul Dhodapkar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | | | - Munivenkatappa Ashok
- ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Pradeep Das Das
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Debasis Biswas
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Usha Kalawat
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | | | - A P Sugunan
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | - Shantanu Prakash
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anirudh K Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Rajamani Barathidasan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | - Subhra Subhadra
- ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | | | - M J Manjunath
- ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Poonam Kanta
- Department of Virology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Nagaraja Mudhigeti
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - Rahul Hazarika
- Regional Medical Research Centre, Dibrugarh, Assam, India
| | - Hricha Mishra
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Kumar Abhishek
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - C Santhalembi
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | - Manas Ranjan Dikhit
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Jitendra Narayan
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Harmanmeet Kaur
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Sidhartha Giri
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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Praharaj I, Jain A, Singh M, Balakrishnan A, Dhodapkar R, Borkakoty B, Ashok M, Das P, Biswas D, Kalawat U, Turuk J, Sugunan AP, Prakash S, Singh AK, Barathidasan R, Subhadra S, Sabat J, Manjunath MJ, Kanta P, Mudhigeti N, Hazarika R, Mishra H, Abhishek K, Santhalembi C, Dikhit MR, Vijay N, Narayan J, Kaur H, Giri S, Gupta N. Authors' response. Indian J Med Res 2021; 153:700-701. [PMID: 34643571 PMCID: PMC8555614 DOI: 10.4103/0971-5916.318158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Ira Praharaj
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Mini Singh
- Department of Virology, Postgraduate Institute of Medical Education & Research, Chandigarh,, India
| | | | - Rahul Dhodapkar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | | | - Munivenkatappa Ashok
- ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Pradeep Das
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Debasis Biswas
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Usha Kalawat
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | | | - A P Sugunan
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | - Shantanu Prakash
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anirudh K Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Rajamani Barathidasan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | - Subhra Subhadra
- ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | | | - M J Manjunath
- ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Poonam Kanta
- Department of Virology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Nagaraja Mudhigeti
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - Rahul Hazarika
- Regional Medical Research Centre, Dibrugarh, Assam, India
| | - Hricha Mishra
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Kumar Abhishek
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - C Santhalembi
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | - Manas Ranjan Dikhit
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Jitendra Narayan
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Harmanmeet Kaur
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Sidhartha Giri
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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Bamra T, Shafi T, Das S, Kumar M, Dikhit MR, Kumar A, Kumar A, Abhishek K, Pandey K, Sen A, Das P. Leishmania donovani Secretory Mevalonate Kinase Regulates Host Immune Response and Facilitates Phagocytosis. Front Cell Infect Microbiol 2021; 11:641985. [PMID: 33981628 PMCID: PMC8110032 DOI: 10.3389/fcimb.2021.641985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/31/2021] [Indexed: 11/13/2022] Open
Abstract
Leishmania secretes over 151 proteins during in vitro cultivation. Cellular functions of one such novel protein: mevalonate kinase is discussed here; signifying its importance in Leishmania infection. Visceral Leishmaniasis is a persistent infection, caused by Leishmania donovani in Indian subcontinent. This persistence is partly due to phagocytosis and evasion of host immune response. The underlying mechanism involves secretory proteins of Leishmania parasite; however, related studies are meagre. We have identified a novel secretory Leishmania donovani glycoprotein, Mevalonate kinase (MVK), and shown its importance in parasite internalization and immuno-modulation. In our studies, MVK was found to be secreted maximum after 1 h temperature stress at 37°C. Its secretion was increased by 6.5-fold in phagolysosome-like condition (pH ~5.5, 37°C) than at pH ~7.4 and 25°C. Treatment with MVK modulated host immune system by inducing interleukin-10 and interleukin-4 secretion, suppressing host’s ability to kill the parasite. Peripheral blood mononuclear cell (PBMC)-derived macrophages infected with mevalonate kinase-overexpressing parasites showed an increase in intracellular parasite burden in comparison to infection with vector control parasites. Mechanism behind the increase in phagocytosis and immunosuppression was found to be phosphorylation of mitogen-activated protein (MAP) kinase pathway protein, Extracellular signal-regulated kinases-1/2, and actin scaffold protein, cortactin. Thus, we conclude that Leishmania donovani Mevalonate kinase aids in parasite engulfment and subvert the immune system by interfering with signal transduction pathways in host cells, which causes suppression of the protective response and facilitates their persistence in the host. Our work elucidates the involvement of Leishmania in the process of phagocytosis which is thought to be dependent largely on macrophages and contributes towards better understanding of host pathogen interactions.
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Affiliation(s)
- Tanvir Bamra
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Taj Shafi
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | | | - Manjay Kumar
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Manas Ranjan Dikhit
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Ajay Kumar
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Ashish Kumar
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Kumar Abhishek
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Krishna Pandey
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Abhik Sen
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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8
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Pandey RK, Dikhit MR, Lokhande KB, Pandey K, Das P, Bimal S. An immunoprophylactic evaluation of Ld-ODC derived HLA-A0201 restricted peptides against visceral leishmaniasis. J Biomol Struct Dyn 2021; 40:6086-6096. [PMID: 33602055 DOI: 10.1080/07391102.2021.1876773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Five (5) HLA-A 0201 restricted epitopes of ornithine decarboxylase derived from Leishmania donovani (Ld-ODC) were examined by reverse vaccinology to develop prophylactics against visceral leishmaniasis (VL). These consensus epitopes comprising (P1: RLMPSAHAI, P2: LLDQYQIHL, P3: GLYHSFNCI, P4: AVLEVLSAL and P5: RLPASPAAL) were observed and presented by diverse HLA alleles screened by immune-informatics tools. These epitopes were also observed for strong stability for appropriate immune response in in silico screening and molecular dynamics. Top five selected epitopes filtered from population coverage analysis and TAP binding affinity were identified and evaluated against treated cases of VL subjects. Experiments were run individually with synthetic peptides or as the cocktail of peptides. A major population of CD8+ T cells were predominantly IFN-γ producers but not the IL-10 cytokines and shown with granzyme-B activity. Therefore, it can be concluded that the screened HLA-A0201 restricted epitope hotspots derived from Leishmania ODC can trigger CD8+ T cells, which can skew other immune cells functions toward protection. However, a detailed analysis can explore its potentiality as a vaccine candidate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Raj Kishor Pandey
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research, Hajipur, India.,Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Manas Ranjan Dikhit
- Department of Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Kiran Bharat Lokhande
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hajipur, India
| | - Krishna Pandey
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Sanjiva Bimal
- Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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9
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Jamal F, Singh MK, Hansa J, Pushpanjali, Ahmad G, Dikhit MR, Umar MS, Bimal S, Das P, Mujeeb AA, Singh SK, Zubair S, Owais M. Corrigendum: Leishmania-Specific Promiscuous Membrane Protein Tubulin Folding Cofactor D Divulges Th 1/Th 2 Polarization in the Host via ERK-1/2 and p38 MAPK Signaling Cascade. Front Immunol 2020; 11:2019. [PMID: 33013858 PMCID: PMC7510234 DOI: 10.3389/fimmu.2020.02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 07/24/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Fauzia Jamal
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Manish K Singh
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Jagadish Hansa
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pushpanjali
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Ghufran Ahmad
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Manas Ranjan Dikhit
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Mohd Saad Umar
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Sanjiva Bimal
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Anzar Abdul Mujeeb
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Shubhankar K Singh
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Swaleha Zubair
- Department of Computer Science, Aligarh Muslim University, Aligarh, India
| | - Mohammad Owais
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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10
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Praharaj I, Jain A, Singh M, Balakrishnan A, Dhodapkar R, Borkakoty B, Ashok M, Das P, Biswas D, Kalawat U, Turuk J, Sugunan A, Prakash S, Singh AK, Barathidasan R, Subhadra S, Sabat J, Manjunath M, Kanta P, Mudhigeti N, Hazarika R, Mishra H, Abhishek K, Santhalembi C, Dikhit MR, Vijay N, Narayan J, Kaur H, Giri S, Gupta N. Pooled testing for COVID-19 diagnosis by real-time RT-PCR: A multi-site comparative evaluation of 5- & 10-sample pooling. Indian J Med Res 2020; 152:88-94. [PMID: 32893844 PMCID: PMC7853252 DOI: 10.4103/ijmr.ijmr_2304_20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND & OBJECTIVES Public health and diagnostic laboratories are facing huge sample loads for COVID-19 diagnosis by real-time reverse transcription-polymerase chain reaction (RT-PCR). High sensitivity of optimized real-time RT-PCR assays makes pooled testing a potentially efficient strategy for resource utilization when positivity rates for particular regions or groups of individuals are low. We report here a comparative analysis of pooled testing for 5- and 10-sample pools by real-time RT-PCR across 10 COVID-19 testing laboratories in India. METHODS Ten virus research and diagnostic laboratories (VRDLs) testing for COVID-19 by real-time RT-PCR participated in this evaluation. At each laboratory, 100 nasopharyngeal swab samples including 10 positive samples were used to create 5- and 10-sample pools with one positive sample in each pool. RNA extraction and real-time RT-PCR for SARS-CoV-2-specific E gene target were performed for individual positive samples as well as pooled samples. Concordance between individual sample testing and testing in the 5- or 10-sample pools was calculated, and the variation across sites and by sample cycle threshold (Ct) values was analyzed. RESULTS A total of 110 each of 5- and 10-sample pools were evaluated. Concordance between the 5-sample pool and individual sample testing was 100 per cent in the Ct value ≤30 cycles and 95.5 per cent for Ctvalues ≤33 cycles. Overall concordance between the 5-sample pooled and individual sample testing was 88 per cent while that between 10-sample pool and individual sample testing was 66 per cent. Although the concordance rates for both the 5- and 10-sample pooled testing varied across laboratories, yet for samples with Ct values ≤33 cycles, the concordance was ≥90 per cent across all laboratories for the 5-sample pools. INTERPRETATION & CONCLUSIONS Results from this multi-site assessment suggest that pooling five samples for SARS-CoV-2 detection by real-time RT-PCR may be an acceptable strategy without much loss of sensitivity even for low viral loads, while with 10-sample pools, there may be considerably higher numbers of false negatives. However, testing laboratories should perform validations with the specific RNA extraction and RT-PCR kits in use at their centres before initiating pooled testing.
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Affiliation(s)
- Ira Praharaj
- Divsion of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Mini Singh
- Department of Virology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | | | - Rahul Dhodapkar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | | | - Munivenkatappa Ashok
- ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Pradeep Das
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Debasis Biswas
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Usha Kalawat
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | | | - A.P. Sugunan
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | - Shantanu Prakash
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anirudh K. Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh, India
| | - Rajamani Barathidasan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | - Subhra Subhadra
- ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | | | - M.J. Manjunath
- ICMR-National Institute of Virology, Bangalore Unit, Bengaluru, Karnataka, India
| | - Poonam Kanta
- Department of Virology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Nagaraja Mudhigeti
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India
| | - Rahul Hazarika
- Regional Medical Research Centre, Dibrugarh, Assam, India
| | - Hricha Mishra
- Department of Microbiology, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Kumar Abhishek
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - C. Santhalembi
- ICMR-National Institute of Virology, Kerala Unit, Alappuzha, Kerala, India
| | - Manas Ranjan Dikhit
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Jitendra Narayan
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Harmanmeet Kaur
- Department of Health Research, Ministry of Health & Family Welfare, New Delhi, India
| | - Sidhartha Giri
- Divsion of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Nivedita Gupta
- Divsion of Epidemiology & Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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11
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Kumar A, Vijaykumar S, Dikhit MR, Abhishek K, Mukherjee R, Sen A, Das P, Das S. Differential Regulation of miRNA Profiles of Human Cells Experimentally Infected by Leishmania donovani Isolated From Indian Visceral Leishmaniasis and Post-Kala-Azar Dermal Leishmaniasis. Front Microbiol 2020; 11:1716. [PMID: 32849363 PMCID: PMC7410929 DOI: 10.3389/fmicb.2020.01716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are small ribonucleic acid that act as an important regulator of gene expression at the molecular level. However, there is no comparative data on the regulation of microRNAs (miRNAs) in visceral leishmaniasis (VL) and post-kala-azar dermal leishmaniasis (PKDL). In this current study, we compared the expression miRNA profile in host cells (GTHP), with VL strain (GVL) and PKDL strain-infected host cell (GPKDL). Normalized read count comparison between different conditions revealed that the miRNAs are indeed differentially expressed. In GPKDL with respect to GVL and GTHP, a total of 798 and 879 miRNAs were identified, out of which 349 and 518 are known miRNAs, respectively. Comparative analysis of changes in miRNA expression suggested that the involvement of differentially expressed miRNAs in various biological processes like PI3K pathway activation, cell cycle regulation, immunomodulation, apoptosis inhibition, different cytokine production, T-cell phenotypic transitions calcium regulation, and so on. A pathway enrichment study using in silico predicted gene targets of differentially expressed miRNAs showed evidence of potentially universal immune signaling pathway effects. Whereas cytokine-cytokine receptor interaction, phagocytosis, and transforming growth factor beta (TGF-β) signaling pathways were more highly enriched using targets of miRNAs upregulated in GPKDL. These findings could contribute to a better understanding of PKDL pathogenesis. Furthermore, the identified miRNAs could also be used as biomarkers in diagnosis, prognosis, and therapeutics of PKDL infection control.
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Affiliation(s)
- Ashish Kumar
- Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Saravanan Vijaykumar
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Manas Ranjan Dikhit
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Kumar Abhishek
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Rimi Mukherjee
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Abhik Sen
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Sushmita Das
- Department of Microbiology, All India Institute of Medical Sciences, Patna, India
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12
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Jamal F, Singh MK, Hansa J, Pushpanjali, Ahmad G, Dikhit MR, Umar MS, Bimal S, Das P, Mujeeb AA, Singh SK, Zubair S, Owais M. Leishmania-Specific Promiscuous Membrane Protein Tubulin Folding Cofactor D Divulges Th 1/Th 2 Polarization in the Host via ERK -1/2 and p38 MAPK Signaling Cascade. Front Immunol 2020; 11:817. [PMID: 32582140 PMCID: PMC7280453 DOI: 10.3389/fimmu.2020.00817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/09/2020] [Indexed: 11/24/2022] Open
Abstract
Visceral leishmaniasis (VL)-related mortality and morbidity imposes a great deal of health concern across the globe. The existing anti-leishmanial drug regimen generally fails to eliminate newly emerging resistant isolates of this dreadful parasite. In such circumstances, the development of a prophylactic strategy to impart protection against the disease is likely to take center stage. In order to develop a promising prophylactic vaccine, it is desirable to identify an adequately potential vaccine candidate. In silico analysis of Leishmania tubulin folding cofactor D protein predicted its potential to activate both B- and T-cell repertoires. Furthermore, the ELISA employing anti-peptide27 (a segment of tubulin folding cofactor D) antibody revealed its proficiency in VL diagnosis and treatment monitoring. The peptide27 and its cocktail with another Leishmania peptide (peptide23) prompted the up-regulation of pro-inflammatory cytokines, such as IFN-γ, TNF-α, IL-2, IL-17, etc., and the down-regulation of immune-regulatory cytokines, such as IL-10, in the immunized BALB/c mice. Coherent to the consequence of peptide-specific humoral immune response, peptide cocktail-based immunization ensued in the predominant amplification of pathogen-specific IgG2a over the IgG1 isotype, up-regulated proliferation of T lymphocytes, and enhanced production of nitric oxide, reactive oxygen species, etc. We also established that the peptide cocktail modulated host MAPK signaling to favor the amplification of Th1-dominated immune response in the host. The peptide cocktail mediated the activation of the host immune armory, which was eventually translated into a significant decline in parasitic load in the visceral organs of experimental animals challenged with Leishmania donovani.
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Affiliation(s)
- Fauzia Jamal
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Manish K Singh
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Jagadish Hansa
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pushpanjali
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Ghufran Ahmad
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Manas Ranjan Dikhit
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Mohd Saad Umar
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Sanjiva Bimal
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Anzar Abdul Mujeeb
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Shubhankar K Singh
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Swaleha Zubair
- Department of Computer Science, Aligarh Muslim University, Aligarh, India
| | - Mohammad Owais
- Interdesciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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13
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Pandey R, Dikhit MR, Kumar A, Dehury B, Pandey K, Topno RK, Das P, Bimal S. Evaluating the immunomodulatory responses of LdODC-derived MHC Class-II restricted peptides against VL. Parasite Immunol 2020; 42:e12699. [PMID: 31976563 DOI: 10.1111/pim.12699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 01/04/2020] [Indexed: 12/14/2022]
Abstract
In a bid to develop a novel immunoprophylactic measure against visceral leishmaniasis (VL), MHC class-II-restricted epitopes of LdODC were identified by reverse vaccinology approach. Five consensus HLA-DRB1*0101-restricted epitopes were screened. The analysis revealed that the set of epitopes was presented by at least 54 diverse MHC class-II alleles. Based on in silico screening, followed by molecular dynamics simulation, population coverage analysis, and HLA cross-presentation ability, five best epitopes were evaluated. PBMCs isolated from treated VL subjects, when stimulated with synthetic peptide alone or as a cocktail of peptides, triggered a secretory IFN-γ, but not the IL-10 level. Support in this notion came from intracellular cytokine level with a considerable up-regulated IFN-γ produced by CD4+ T cells. Also, the enhanced IFN-γ seemed to be augmented with the activation of macrophages with prominent IL-12 production. Therefore, it can be concluded that the screened MHC class-II-restricted epitope hotspots derived from Leishmania ODC can trigger CD4+ T cells, which can skew macrophage functions towards protection. However, a detailed analysis can explore its potentiality as a vaccine candidate.
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Affiliation(s)
- RajKishor Pandey
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research, Hajipur, India.,Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Manas Ranjan Dikhit
- Department of Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Avinash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research, Hajipur, India
| | - Budheswar Dehury
- Department of Bioinformatics, ICMR-RMRC, Government of India, Bhubaneswar, India
| | - Krishna Pandey
- Departmentof Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Roshan Kamal Topno
- Departmentof Epidemiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Sanjiva Bimal
- Division of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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14
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Siddiqui NA, Pandey K, R Das VN, Sinha SK, Verma RB, Lal CS, Ali V, Topno RK, Dikhit MR, Das P. Magnitude of unreported kala-azar cases in a highly endemic district of Bihar, India: A positive impact of Indian elimination programme. J Vector Borne Dis 2019; 56:315-322. [PMID: 33269731 DOI: 10.4103/0972-9062.302034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND & OBJECTIVES In India, kala-azar surveillance is weak and no public-private partnership exists for disease containment. Estimate of disease burden is not reliably available and still cases are going to private providers for the treatment. The present study aimed to assess the magnitude of kala-azar cases actually detected and managed at private set-up and unreported to existing health management information system. METHODS Institution based cross-sectional prospective pilot study was conducted. List of facilities was created with the help of key informants. The information about incidence of kala-azar cases were captured on monthly basis from July 2010 to June 2011. Rapid diagnostic strip test (rk-39) or bone marrow/splenic puncture were applied as laboratory methods for the diagnosis of kala-azar. Descriptive statistics as well as chi-square test for comparison between proportions was conducted. RESULTS Overall availability of private practitioners (PPs) was 4.59/1,00,000 population and maximum PPs (46; 93.9%) were from qualified category. The median years of medical practice was 25 yr (inter quartile-range [18, 28]). Interestingly, only a small proportion (240; 19%) of cases was managed by PPs. Amongst the PPs, only low proportion (32; 18.2%) managed >2 cases per month. The mean number of kala-azar suspects and cases identified varied significantly between different PPs' professions with p <0.048 and p <0.032, respectively. A highly significant difference (p <0.0001) was observed for kala-azar case load between qualified and unqualified practitioners. A small proportion (38; 15.8%) of kala-azar cases was not present in the public health system record. INTERPRETATION & CONCLUSION Still sizeable proportions of cases are going to PPs and unrecorded into government surveillance system. A mechanism need to be devised to involve at least qualified PPs in order to reduce treatment delay and increase case detection in the region.
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Affiliation(s)
- N A Siddiqui
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - K Pandey
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - V N R Das
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - S K Sinha
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - R B Verma
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - C S Lal
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - V Ali
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - R K Topno
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - M R Dikhit
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
| | - P Das
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, Bihar, India
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15
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Topno RK, Pandey K, Singh BB, Dikhit MR, Kumar A, Kumar M, Sahoo GC, Rabidas VN, Siddiqui NA, Paswan W, Lal A, Dinesh DS, Das P. Viral Etiological Factors Causing Acute Encephalitis Syndrome (AES) In Gaya Division, India. Hosp Pract Res 2019. [DOI: 10.15171/hpr.2019.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background: From Gaya and adjoining regions, the trend in patients admitted with acute neurological illness was investigated. Illnesses were identified as sudden outbreaks of Japanese virus encephalitis (JE), Herpes simplex virus encephalitis (HSV1&2), and other acute encephalitis syndrome (AES). Objective: In the current study, an investigation was carried out to assess potential infectious pathogens in patients aged 16 years or younger who were admitted to Anugrah Narayan Magadh Memorial Medical College Hospital, Gaya, with encephalitis-like symptoms. Methods: Cross-epidemiological, serological, and molecular biological studies were performed on samples collected from 71 patients below 16 years of age. Patients’ clinical histories, i.e. fever, socio-demographic characteristics, and other clinical data, were extracted from patient files. Results: The results showed confirmed AES cases, including 49.30% JE and 7.04% HSV positive patients. A higher casefatality rate of 40% in JE and 40% HSV cases below 7 years of age were observed during treatment would become an unavoidable concern. The epidemical sex ratio was observed to be higher in girls than in boys (1.26:1). Conclusion: The results suggested that JE virus was found to be a main causative risk factor responsible for disease transmission in the outbreak area.
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Affiliation(s)
- Roshan Kamal Topno
- Department of Epidemiology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Krishna Pandey
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Banke Bihari Singh
- Department of Pediatrics, Anugrah Narayan Magadh Memorial Medical College Hospital, Gaya- 823001, India
| | - Manas Ranjan Dikhit
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Ashish Kumar
- Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Maneesh Kumar
- Department of Virology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Ganesh Chandra Sahoo
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Vidya Nand Rabidas
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Niyamat Ali Siddiqui
- Department of Bio-Statistics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Wakil Paswan
- Department of Pediatrics, Anugrah Narayan Magadh Memorial Medical College Hospital, Gaya- 823001, India
| | - Arjun Lal
- Department of Microbiology, Anugrah Narayan Magadh Memorial Medical College Hospital, Gaya-823001, India
| | - Diwakar Singh Dinesh
- Department of Vector Biology and Control, ICMR- Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
| | - Pradeep Das
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna-800007, India
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16
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Kumar M, Topno RK, Dikhit MR, Bhawana, Sahoo GC, Madhukar M, Pandey K, Das P. Molecular docking studies of chloroquine and its derivatives against P23 pro-zbd domain of chikungunya virus: Implication in designing of novel therapeutic strategies. J Cell Biochem 2019; 120:18298-18308. [PMID: 31310373 DOI: 10.1002/jcb.29139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 01/26/2023]
Abstract
The arthropod-transmitted chikungunya virus has emerged as an epidemic menace that causes debilitating polyarthritis. With this life-threatening impact on humans, the possible treatment requires to cure the viral infectivity. But, devoid of any vaccine against the chikungunya virus (CHIKV), there is a need to develop a novel chemotherapeutic strategy to treat this noxious infection. CHIKV carries highly compact P23pro-zbd structure that possesses potential RNA-binding surface domains which extremely influences the use of RNA template during genome replication at the time of infection and pathogenesis. Therefore, computational approaches were used to explore the novel small molecule inhibitors targeting P23pro-zbd domain. The tertiary structure was modeled and optimized using in silico approaches. The results obtained from PROCHECK (93.1% residues in favored regions), ERRAT (87.480 overall model quality) and ProSA (Z-score: -11.72) revealed the reliability of the proposed model. Interestingly, a previously reported inhibitor, chloroquine possesses good binding affinities with the target domain. In-depth analysis revealed that chloroquine derivatives such as didesethyl chloroquine hydroxyacetamide, cletoquine, hydroxychloroquine exhibited a better binding affinity. Notably, MD simulation analysis exhibited that Thr1312, Ala1355, Ala1356, Asn1357, Asp1364, Val1366, Cys1367, Ala1401, Gly1403, Ser1443, Tyr1444, Gly1445, Asn1459, and Thr1463 residues are the key amino acid responsible for stable ligand-protein interaction. The results obtained from this study provide new insights and advances the understanding to develop a new approach to consider effective and novel drug against chikungunya. However, a detailed in vivo study is required to explore its drug likeliness against this life-threatening disease.
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Affiliation(s)
- Maneesh Kumar
- Department of Virology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Roshan Kamal Topno
- Department of Epidemiology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Manas Ranjan Dikhit
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Bhawana
- Department of Virology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Ganesh Chandra Sahoo
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Major Madhukar
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Krishna Pandey
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
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Chauhan AS, Sahoo GC, Dikhit MR, Das P. Acid-Sensing Ion Channels Structural Aspects, Pathophysiological Importance and Experimental Mutational Data Available Across Various Species to Target Human ASIC1. Curr Drug Targets 2018; 20:111-121. [DOI: 10.2174/1389450119666180820103316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 08/01/2018] [Accepted: 08/15/2018] [Indexed: 01/16/2023]
Abstract
The H+-gated (proton) currents are widely present in brain sensory neuronal system and
various studies identified the structural units and deciphered the physiological and pathological function
of ion channels. The normal neuron requires an optimal pH to carry out its functions. In acidosis,
the ASICs (Acid-sensing Ion Channels) are activated in both the CNS (central nervous system) and
PNS (peripheral nervous system). ASICs are related to degenerin channels (DEGs), epithelial sodium
cation channels (ENaCs), and FMRF-amide (Phe-Met-Arg-Phe-NH2)-gated channels (FaNaC). Its activation
leads physiologically to pain perception, synaptic plasticity, learning and memory, fear,
ischemic neuronal injury, seizure termination, neuronal degeneration, and mechanosensation. It detects
the level of acid fluctuation in the extracellular environment and responds to acidic pH by increasing
the rate of membrane depolarization. It conducts cations like Na+ (Sodium) and Ca2+ (Calcium)
ions across the membrane upon protonation. The ASICs subtypes are characterized by differing
biophysical properties and pH sensitivities. The subtype ASIC1 is involved in various CNS diseases
and therefore focusing on its specific functional properties will guide in drug design methods. The review
highlights the cASIC1 (Chicken ASIC1) crystal structures, involvement in physiological environment
and limitations of currently available inhibitors. In addition, it details the mutational data
available to design an inhibitor against hASIC1 (Human ASIC1).
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Affiliation(s)
- Anurag Singh Chauhan
- Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences (Indian Council of Medical Research), Agamkuan, Patna- 800 007, Bihar, India
| | - Ganesh Chandra Sahoo
- Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences (Indian Council of Medical Research), Agamkuan, Patna- 800 007, Bihar, India
| | - Manas Ranjan Dikhit
- Biomedical Informatics, Rajendra Memorial Research Institute of Medical Sciences (Indian Council of Medical Research), Agamkuan, Patna- 800 007, Bihar, India
| | - Pradeep Das
- Department of Molecular Parasitology, Rajendra Memorial Research Institute of Medical Sciences (Indian Council of Medical Research), Agamkuan, Patna- 800 007, Bihar, India
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Topno RK, Shankar V, Dikhit MR, Madhukar M, Pandey K, Das VNR, Kumar M, Kumar B, Agrawal K, Siddiqui NA, Sahoo GC, Kumar R, Singh AK, Kumar R, Singh D, Das P. Noninvasive Sweat-Based Diagnosis of Visceral Leishmaniasis and Post Kala-Azar Dermal Leishmaniasis. Am J Trop Med Hyg 2018; 99:1162-1164. [PMID: 30203740 PMCID: PMC6221248 DOI: 10.4269/ajtmh.17-0749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 06/28/2018] [Indexed: 01/16/2023] Open
Abstract
The diagnosis of visceral leishmaniasis (VL) is one of the foremost barriers in the control of this disease, as demonstration of the parasite by splenic/bone marrow aspiration is relatively difficult and requires expertise and laboratory support. The aim of the present study was to find a noninvasive diagnostic approach using the existing recombinant kinesine-39 (rK-39) immunochromatographic nitrocellulose strips test (ICT) with a human sweat specimen for the diagnosis of VL. The investigation was carried out on specimens (blood, sweat, and urine) collected from 58 confirmed VL, 50 confirmed post kala-azar dermal leishmaniasis (PKDL), 36 healthy control, and 35 patients from other diseases. The data obtained from this study reveal that 96.6% clinically confirmed active VL participants were found to be positive when tested against a sweat specimen. Interestingly, the scenario was similar when tested against a blood specimen (96.6% positive by rK-39). Moreover, a test of both sweats and blood specimens from 50 PKDL participants resulted in 100% positivity, whereas no healthy control participants were found to be rK-39 positive. The sensitivity of the rK-39 ICT in sweat specimen was 94.7%, whereas the specificity was 100% in healthy controls from endemic, nonendemic, and other infectious diseases, respectively. No difference was observed in sweat specimen of VL and PKDL cases which signifies its reliability. However, further evaluation of this method on a larger scale could enhance the reliability of the proposed model so that it could be used efficiently in VL management and eradication.
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Affiliation(s)
- Roshan Kamal Topno
- Department of Epidemiology, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Vikas Shankar
- Department of Skin and VD, Nalanda Medical College and Hospital, Patna, India
| | - Manas Ranjan Dikhit
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Major Madhukar
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Krishna Pandey
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - V. N. R. Das
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Maneesh Kumar
- Department of Virology, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Bipin Kumar
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Kanhaiya Agrawal
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Niyamat Ali Siddiqui
- Department of Biostatistics, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Ganesh Chandra Sahoo
- Department of Bioinformatics, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Rishikesh Kumar
- Department of Virology, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Ashish Kumar Singh
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Rajeev Kumar
- Department of Community Medicine, Nalanda Medical College and Hospital, Patna, India
| | - Dharmendra Singh
- Department of Biochemistry, National JALMA institute for Leprosy and other Mycobacterial Disease (ICMR), Agra, India
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
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Dikhit MR, Das S, Mahantesh V, Kumar A, Singh AK, Dehury B, Rout AK, Ali V, Sahoo GC, Topno RK, Pandey K, Das VNR, Bimal S, Das P. The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response. Sci Rep 2018; 8:14175. [PMID: 30242172 PMCID: PMC6154976 DOI: 10.1038/s41598-018-32040-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 08/14/2018] [Indexed: 12/12/2022] Open
Abstract
To explore new protective measure against visceral leishmaniasis, reverse vaccinology approach was employed to identify key immunogenic regions which can mediate long-term immunity. In-depth computational analysis revealed nine promiscuous epitopes which can possibly be presented by 46 human leukocyte antigen, thereby broadening the worldwide population up to 94.16%. This is of reasonable significance that most of the epitopes shared 100% sequence homology with other Leishmania species and could evoke a common pattern of protective immune response. Transporter associated with antigen processing binding affinity, molecular docking approach followed by dynamics simulation and human leukocyte antigen stabilization assay suggested that the best five optimal set of epitopes bind in between α1 and α2 binding groove with sufficient affinity and stability which allows the translocation of intact epitope to the cell surface. Fascinatingly, the human leukocyte antigen stabilization assay exhibited a modest correlation with the positive immunogenicity score predicted by class I pMHC immunogenicity predictor. A support for this notion came from ELISA and FACS analysis where the epitopes as a cocktail induced CD8+ IFN-γ and Granzyme B levels significantly in treated visceral leishmaniasis subject which suggests the immunogenic ability of the selected epitopes.
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Affiliation(s)
- Manas Ranjan Dikhit
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India.,Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Sushmita Das
- Department of Microbiology, All India Institute of Medical Sciences, Patna, 801507, Bihar, India
| | - Vijaya Mahantesh
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Akhilesh Kumar
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Ashish Kumar Singh
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Budheswar Dehury
- BioMedical Informatics Centre, ICMR-Regional Medical Research Centre, Bhubaneswar, 751023, Odisha, India
| | - Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, West Bengal, India
| | - Vahab Ali
- Department of Clinical Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Ganesh Chandra Sahoo
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Roshan Kamal Topno
- Department of Epidemiology, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Krishna Pandey
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - V N R Das
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Sanjiva Bimal
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India
| | - Pradeep Das
- Department of Molecular Parasitology, Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, 800007, Bihar, India.
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Kumar A, Dikhit MR, Amit A, Zaidi A, Pandey RK, Singh AK, Suman SS, Ali V, Das VNR, Pandey K, kumar V, Singh SK, Narayan S, Chourasia HK, Das P, Bimal S. Immunomodulation induced through ornithine decarboxylase DNA immunization in Balb/c mice infected with Leishmania donovani. Mol Immunol 2018; 97:33-44. [DOI: 10.1016/j.molimm.2018.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 12/21/2022]
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Dikhit MR, Kumar A, Das S, Dehury B, Rout AK, Jamal F, Sahoo GC, Topno RK, Pandey K, Das VNR, Bimal S, Das P. Identification of Potential MHC Class-II-Restricted Epitopes Derived from Leishmania donovani Antigens by Reverse Vaccinology and Evaluation of Their CD4+ T-Cell Responsiveness against Visceral Leishmaniasis. Front Immunol 2017; 8:1763. [PMID: 29312304 PMCID: PMC5735068 DOI: 10.3389/fimmu.2017.01763] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/27/2017] [Indexed: 01/09/2023] Open
Abstract
Visceral leishmaniasis (VL) is one of the most neglected tropical diseases for which no vaccine exists. In spite of extensive efforts, no successful vaccine is available against this dreadful infectious disease. To support vaccine development, an immunoinformatics approach was applied to screen potential MHC class-II-restricted epitopes that can activate the immune cells. Initially, 37 epitopes derived from six stage-dependent, overexpressed antigens were predicted, which were presented by at least 26 diverse MHC class-II allele. Based on a population coverage analysis and human leukocyte antigen cross-presentation ability, six of the 37 epitopes were selected for further analysis. Stimulation with synthetic peptide alone or as a cocktail triggered intracellular IFN-γ production. Moreover, specific IgG antibodies were detected in the serum of active VL cases against P1, P4, P5, and P6 in order to evaluate the peptide effect on the humoral immune response. Additionally, most of the peptides, except P2, were found to be non-inducers of CD4+ IL-10 against both active VL as well as treated VL subjects. This finding suggests there is no role of these peptides in the pathogenesis of Leishmania. Peptide immunogenicity was validated in BALB/c mice immunized with a cocktail of synthetic peptide emulsified in complete Freund’s adjuvant/incomplete Freund’s adjuvant. The immunized splenocytes induced strong spleen cell proliferation upon parasite re-stimulation. Furthermore, increased IFN-γ, interleukin-12, IL-17, and IL-22 production augmented with elevated nitric oxide (NO) synthesis is thought to play a crucial role in macrophage activation. In this investigation, we identified six MHC class-II-restricted epitope hotspots of Leishmania antigens that induce CD4+ Th1 and Th17 responses, which could be used to potentiate a human universal T-epitope vaccine against VL.
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Affiliation(s)
- Manas Ranjan Dikhit
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Patna, India.,Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Akhilesh Kumar
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Sushmita Das
- Department of Microbiology, All India Institute of Medical Sciences, Patna, India
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Odisha, India
| | - Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Kolkata, India
| | - Fauzia Jamal
- Department of Microbiology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Ganesh Chandra Sahoo
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Roshan Kamal Topno
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Krishna Pandey
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - V N R Das
- Department of Clinical Medicine, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Sanjiva Bimal
- Department of Immunology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | - Pradeep Das
- Department of Molecular Parasitology, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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Ansari MY, Dikhit MR, Sahoo GC, Ali V, Das P. Recent advancement and treatment of leishmaniasis based on pharmacoinformatics approach: Current and future outlook. Gene Reports 2017. [DOI: 10.1016/j.genrep.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Chauhan AS, Ansari MY, Mansuri R, Dikhit MR, Ali V, Sahoo GC, Das P. Computational elucidation, mutational and hot spot-based designing of potential inhibitors against human acid-sensing ion channels (hASIC-1a) to treat various physiological conditions. J Biomol Struct Dyn 2017; 36:3513-3530. [PMID: 29039242 DOI: 10.1080/07391102.2017.1392364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Acid-sensing ion channels are ligand/proton-gated ion channels belonging to the family of the degenerin/epithelial Na+ channel (DEG/ENaC). They function as a sodium-selective pore for Ca2+ entry into neuronal cells during pathological conditions. The blocking of this channel has therapeutic importance, because at basal physiological pH (7.2), it is in a closed state and under a more acidic condition, and the ASIC1a ion channel is activated. To investigate the different states of the hASIC1a channel based on mutational analysis, structure-based virtual screening and molecular dynamics simulation studies. The system showed stability after 30 ns (after 1500 frame), and it was stabilized to an average value around 2.2Å. During the simulation, the ion channel residues in persistent contact with toxin PcTx1 were D237, E238, D347, D351, E219 and E355. These residues are important physiologically for the activation of the channel. From in silico alanine scanning, the significant hotspots obtained in hASIC1 are E344, P347, F352, D351, E355 and E219. From the sitemap analysis, it was evident that the sitemap found one of the active sites at the PcTx1 binding site with a site score of 1.086 and a D-score of 1.035 for hASIC1. We obtained a few promising hits and final potential hits from the virtual screening in hASIC1 that made interactions with the residues in the acidic pocket (E344, P347, F352, D351, E355 and E219). Based on these studies, the hits and scaffolds of potential therapeutic interest against various pathological conditions are associated with hASIC1a for future studies.
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Affiliation(s)
- Anurag Singh Chauhan
- a Biomedical Informatics, Indian Council of Medical Research , Rajendra Memorial Research Institute of Medical Sciences , Agamkuan, Patna 800 007 , Bihar , India.,d Department of Pharmacoinformatics , National Institute of Pharmaceutical Education and Research , Hajipur 844 102 , Bihar , India
| | - Md Yousuf Ansari
- b Deparment of Pharmaceutical Chemistry , M.M. College of Pharmacy, Maharishi Markandeshwar University , Mullana 133207 , Haryana , India.,d Department of Pharmacoinformatics , National Institute of Pharmaceutical Education and Research , Hajipur 844 102 , Bihar , India
| | - Rani Mansuri
- a Biomedical Informatics, Indian Council of Medical Research , Rajendra Memorial Research Institute of Medical Sciences , Agamkuan, Patna 800 007 , Bihar , India.,d Department of Pharmacoinformatics , National Institute of Pharmaceutical Education and Research , Hajipur 844 102 , Bihar , India
| | - Manas Ranjan Dikhit
- a Biomedical Informatics, Indian Council of Medical Research , Rajendra Memorial Research Institute of Medical Sciences , Agamkuan, Patna 800 007 , Bihar , India
| | - Vahab Ali
- a Biomedical Informatics, Indian Council of Medical Research , Rajendra Memorial Research Institute of Medical Sciences , Agamkuan, Patna 800 007 , Bihar , India
| | - Ganesh Chandra Sahoo
- a Biomedical Informatics, Indian Council of Medical Research , Rajendra Memorial Research Institute of Medical Sciences , Agamkuan, Patna 800 007 , Bihar , India
| | - Pradeep Das
- c Department of Molecular Parasitology, Indian Council of Medical Research , Rajendra Memorial Research Institute of Medical Sciences , Agamkuan, Patna 800 007 , Bihar , India
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Jamal F, Dikhit MR, Singh MK, Shivam P, Kumari S, Pushpanjali S, Dubey AK, Kumar P, Narayan S, Gupta AK, Pandey K, Das VNR, Bimal S, Das P, Singh SK. Identification of B-cell Epitope of Leishmania donovani and its application in diagnosis of visceral leishmaniasis. J Biomol Struct Dyn 2016; 35:3569-3580. [PMID: 27892844 DOI: 10.1080/07391102.2016.1263240] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Diagnosis of visceral leishmaniasis (VL) is often hindered by cross-reactions with antigens from other related parasite infections. This study aimed to develop an immunochromatographic test (ICT) which can detect the antigen present in circulating immune complexes (CICs) of VL patients using B-cell epitope-specific antibodies. MS analysis of six immunoreactive 2DE spots revealed two epitopes i.e. RFFVQGDGIGQHSLQEALERR (P1) and RRVAVLVLLDRL (P2) (From a hypothetical protein [Acc No: XP_003861458.1]). The epitope conservancy analysis suggested that the linear epitope (P1P2) is 97-100% conserved among Leishmania species and diverged from Homo sapiens (61% query coverage and 80% identity). Further, immunoinformatics analysis of hydrophilicity and flexibility confirmed the antigenicity of the peptide fragment. The linear epitope (P1P2) was synthesized (98% purity) and the purity was confirmed by high-performance liquid chromatography and MS. The indirect Enzyme linked immunosorbent assay results confirmed the presence of the corresponding antibody in VL patient's sera but not in those of healthy and other diseases. The result demonstrated a sensitivity 90%; Se Cl95% (82.16-96.27)% and specificity 100%; Sp Cl95% (84.56-100)% which indicated the possibility to be used as a diagnostic tool. Sensitivity, specificity, and diagnostic efficiency of colloidal gold conjugated anti-P1P2 antibody ICT strip was 100, 95.2, and 96.7%, respectively, which is slightly better as compared to other ICT for VL. Though, our result indicated the utility of anti-P1P2 antibody to detect CICs epitopes, a large-scale inspection in endemic and non-endemic area and in different ethnic population is needed for its validation and authentication.
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Affiliation(s)
- Fauzia Jamal
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Manas Ranjan Dikhit
- b Department of Bioinformatics , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Manish K Singh
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Pushkar Shivam
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Sarita Kumari
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Sinha Pushpanjali
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Amit K Dubey
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India.,c Department of Biotechnology , National Institute of Pharmaceutical Education and Research , Hajipur 844102 , India
| | - Prakash Kumar
- c Department of Biotechnology , National Institute of Pharmaceutical Education and Research , Hajipur 844102 , India
| | - Shyam Narayan
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Anil K Gupta
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Krishna Pandey
- d Department of Clinical Medicine , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - V N R Das
- d Department of Clinical Medicine , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Sanjiva Bimal
- e Department of Immunology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Pradeep Das
- f Department of Molecular Biology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
| | - Shubhankar K Singh
- a Department of Microbiology , Rajendra Memorial Research Institute of Medical Sciences , Patna 800007 , India
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Ansari MY, Equbal A, Dikhit MR, Mansuri R, Rana S, Ali V, Sahoo GC, Das P. Establishment of correlation between in-silico and in-vitro test analysis against Leishmania HGPRT to inhibitors. Int J Biol Macromol 2015; 83:78-96. [PMID: 26616453 DOI: 10.1016/j.ijbiomac.2015.11.051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/13/2015] [Accepted: 11/18/2015] [Indexed: 10/22/2022]
Abstract
Hypoxanthine Phosphoribosyltransferase (HGPRT; EC 2.4.2.8) is a central enzyme in the purine recycling pathway of all protozoan parasites. Protozoan parasites cannot synthesize purine bases (DNA/RNA) which is essential for survival as lack of de-novo pathway. Thus its good target for drug design and discovery as inhibition leads to cessation of replication. PRTase (transferase enzyme) has common PRTase type I folding pattern domain for its activities. Genomic studies revealed the sequence pattern and identified highly conserved residues that catalyzed the reaction in protozoan parasites. A recombinant protein has 24 kDa molecular mass (rLdHGPRT) was cloned, expressed and purified for testing of guanosine monophosphate (GMP) analogous compounds in-vitro by spectroscopically to the rLdHGPRT, lysates protein and MTT assay on Leishmania donovani. The predicted inhibitors of different libraries were screen into FlexX. The reported inhibitors were tested in-vitro. The 2'-deoxyguanosine 5'-diphosphate (DGD) (IC50 value 12.5 μM) is two times more effective when compared to guanosine-5'-diphosphate sodium (GD). Interestingly, LdHGPRT complex has shown stable after 24 ns in molecular dynamics simulation with interacting amino acids are Glu125, Ile127, Lys87 and Val186. QSAR studies revealed the correlation between predicted and experimental values has shown R2 0.998. Concludes that inversely proportional to their docked score with activities.
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Affiliation(s)
- Md Yousuf Ansari
- Pharmacoinformatics Department, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, India; BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Asif Equbal
- Biochemistry Department, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Manas Ranjan Dikhit
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Rani Mansuri
- Pharmacoinformatics Department, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, India; BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Sindhuprava Rana
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Vahab Ali
- Biochemistry Department, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Ganesh Chandra Sahoo
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India.
| | - Pradeep Das
- Pharmacoinformatics Department, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, India; BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
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Das P, Amit A, Singh SK, Chaudhary R, Dikhit MR, yadav A, Pandey K, Das VNR, Sundram S, Das P, Bimal S. Leishmania donovani phosphoproteins pp41 and pp29 re-establishes host protective immune response in visceral leishmaniasis. Parasitol Int 2015; 64:18-25. [DOI: 10.1016/j.parint.2014.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 08/07/2014] [Accepted: 08/30/2014] [Indexed: 10/24/2022]
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Yadav A, Amit A, Chaudhary R, Chandel AS, Mahantesh V, Suman SS, Singh SK, Dikhit MR, Ali V, Rabidas V, Pandey K, Kumar A, Das P, Bimal S. Leishmania donovani: impairment of the cellular immune response against recombinant ornithine decarboxylase protein as a possible evasion strategy of Leishmania in visceral leishmaniasis. Int J Parasitol 2015; 45:33-42. [DOI: 10.1016/j.ijpara.2014.08.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/05/2014] [Accepted: 08/07/2014] [Indexed: 01/17/2023]
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Anwar S, Dikhit MR, Singh KP, Kar RK, Zaidi A, Sahoo GC, Roy AK, Nozaki T, Das P, Ali V. Interaction between Nbp35 and Cfd1 proteins of cytosolic Fe-S cluster assembly reveals a stable complex formation in Entamoeba histolytica. PLoS One 2014; 9:e108971. [PMID: 25271645 PMCID: PMC4182839 DOI: 10.1371/journal.pone.0108971] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 08/29/2014] [Indexed: 02/01/2023] Open
Abstract
Iron-Sulfur (Fe-S) proteins are involved in many biological functions such as electron transport, photosynthesis, regulation of gene expression and enzymatic activities. Biosynthesis and transfer of Fe-S clusters depend on Fe-S clusters assembly processes such as ISC, SUF, NIF, and CIA systems. Unlike other eukaryotes which possess ISC and CIA systems, amitochondriate Entamoeba histolytica has retained NIF & CIA systems for Fe-S cluster assembly in the cytosol. In the present study, we have elucidated interaction between two proteins of E. histolytica CIA system, Cytosolic Fe-S cluster deficient 1 (Cfd1) protein and Nucleotide binding protein 35 (Nbp35). In-silico analysis showed that structural regions ranging from amino acid residues (P33-K35, G131-V135 and I147-E151) of Nbp35 and (G5-V6, M34-D39 and G46-A52) of Cfd1 are involved in the formation of protein-protein complex. Furthermore, Molecular dynamic (MD) simulations study suggested that hydrophobic forces surpass over hydrophilic forces between Nbp35 and Cfd1 and Van-der-Waal interaction plays crucial role in the formation of stable complex. Both proteins were separately cloned, expressed as recombinant fusion proteins in E. coli and purified to homogeneity by affinity column chromatography. Physical interaction between Nbp35 and Cfd1 proteins was confirmed in vitro by co-purification of recombinant Nbp35 with thrombin digested Cfd1 and in vivo by pull down assay and immunoprecipitation. The insilico, in vitro as well as in vivo results prove a stable interaction between these two proteins, supporting the possibility of its involvement in Fe-S cluster transfer to target apo-proteins through CIA machinery in E. histolytica. Our study indicates that initial synthesis of a Fe-S precursor in mitochondria is not necessary for the formation of Cfd1-Nbp35 complex. Thus, Cfd1 and Nbp35 with the help of cytosolic NifS and NifU proteins can participate in the maturation of non-mitosomal Fe-S proteins without any apparent assistance of mitosomes.
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Affiliation(s)
- Shadab Anwar
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agam-kuan, Patna, India
| | - Manas Ranjan Dikhit
- Department of Biomedical Informatics Centre, Rajendra Memorial Research Institute of Medical Sciences, Agam-kuan, Patna, India
| | - Krishn Pratap Singh
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agam-kuan, Patna, India
| | - Rajiv Kumar Kar
- Department of Biomedical Informatics Centre, Rajendra Memorial Research Institute of Medical Sciences, Agam-kuan, Patna, India
| | - Amir Zaidi
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agam-kuan, Patna, India
| | - Ganesh Chandra Sahoo
- Department of Biomedical Informatics Centre, Rajendra Memorial Research Institute of Medical Sciences, Agam-kuan, Patna, India
| | | | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Pradeep Das
- Department of Molecular Biology, Rajendra Memorial Research Institute of Medical Sciences, Agam-kuan, Patna, India
| | - Vahab Ali
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, Rajendra Memorial Research Institute of Medical Sciences, Agam-kuan, Patna, India
- * E-mail:
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Sahoo GC, Rani M, Ansari MY, Jha C, Rana S, Dikhit MR, Moharana KC, Kumar R, Das P. Structure, evolution and virtual screening of NDM-1 strain from Kolkata. ACTA ACUST UNITED AC 2014; 10:235-63. [DOI: 10.1504/ijbra.2014.060761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sahoo GC, Ansari MY, Dikhit MR, Gupta N, Rana S, Das P. Computational Identification of microRNA-like Elements in Leishmania major. Microrna 2014; 2:225-230. [PMID: 25069447 DOI: 10.2174/2211536602666131203232422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 11/05/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
Leishmaniasis represents endemic infections that occur predominantly, in tropical and sub-tropical regions. The current situation for the chemotherapy of leishmaniasis is more promising than it has been for several decades with both new drugs and new formulations of old drugs either recently approved or in clinical trials. Investigations focused on parasite biology and identification of novel drug targets have become of great importance. The identification and characterization of microRNA (miRNAs) in the parasite and their possible biological action hopefully facilitate the discovery of potential antiparasitic drug targets against leishmaniasis. microRNA and other small RNA transcripts are derived from distinct loci in the genome and play critical roles in RNA-mediated gene silencing mechanisms in the organisms. miRNAs regulate mRNA stability through perfect and imperfect match to the targets. The biological activities of miRNAs have been related to many biological events, from resistant to microbe infections to cellular differentiation. miRNA like-elements have been identified in Leishmania major. Identification of miRNA-like elements in L. major provides a foundation for subsequent functional studies. Computational strategies provide an efficient manner to predict miRNA genes and their targets. Twenty-five potential miRNA-like elements in different chromosomes (chr.) like chr. 7(th), 8(th), 17(th), 18(th), 21(st), 23(rd), 25(th), 26(th), 29(th), 31(st), 32(nd), 33(rd), 34(th) and 35(th) of L. major have been identified. It is known from this study that the target genes of miRNA-like elements involve multidrug resistant protein such as ABC transporter, ribosomal protein, RNA binding proteins, hydrolase and exonuclease.
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Affiliation(s)
| | | | | | | | | | - Pradeep Das
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam kuan, Patna-800007, India
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Chandra Sahoo G, Yousuf Ansari M, Rana S, Ranjan Dikhit M, Kamal Topno R, Pandey K, Das P. Molecular Modeling and Ligand-Protein Interaction of N-Protein of Chandipura Virus. LETT DRUG DES DISCOV 2013. [DOI: 10.2174/15701808113109990070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sahoo GC, Yousuf Ansari M, Dikhit MR, Kannan M, Rana S, Das P. Structure prediction of gBP21 protein ofL. donovaniand its molecular interaction. J Biomol Struct Dyn 2013; 32:709-29. [DOI: 10.1080/07391102.2013.789400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
UNLABELLED There has been a revival of interest in Cysteine protease for Visceral Leishmaniasis (VL) attributed to massive outbreaks of leishmaniasis in the tropical region. The cysteine protease database (CPDB) was designed to find data related to cysteine protease (CP) of different species of Leishmania and Trypanosoma brucei in a single platform. This has reflected in substantial increase in the submission of Leishmania genome sequences to NCBI (National Center for Biotechnology Information) database. The CPDB database aims to provide a summary of data analysis, such as physiochemical and molecular properties, proteolytic cleavage sites, classification into functional families using SVMProt and other ExPASy tools. The main aim of this database is to provide different protein inhibitors of cysteine protease groups that were collected from literature and make available their 3-D structures through JMol with JAVA platform. These CP inhibitors are freely downloadable and also have added links for functional analyses of other proteins, which is helpful for users. All this information in CPDB, a single platform, will prove to be of great help for researchers who are involved in drug discovery and analysis of other physiochemical and molecular properties of the protein. AVAILABILITY the database is available for free at.
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Affiliation(s)
- Sindhuprava Rana
- Biomedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India800007.
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Kar RK, Suryadevara P, Sahoo BR, Sahoo GC, Dikhit MR, Das P. Exploring novel KDR inhibitors based on pharmaco-informatics methodology. SAR QSAR Environ Res 2013; 24:215-234. [PMID: 23437769 DOI: 10.1080/1062936x.2013.765912] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Kinase-insert domain-containing receptor (KDR) is one of the important mediators of Vascular endothelial growth factor (VEGF) function in endothelial cells. Inhibition of KDR can be therapeutically advantageous for treatment of a number of diseases. The present study focuses on exploring novel KDR inhibitors by means of pharmaco-informatics methodologies. Three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis by atom-based pharmacophore mapping over a set of 85 molecules provides a proposition regarding the molecular fingerprint that can be optimized for designing more active inhibitors. The model was statistically validated with Q(2) = 0.865 for training and r(2) = 0.789, Pearson-r = 0.903 for test set molecules; r(2)(0.925) by external validation suggests model robustness and indicates it as a strong query for screening any compound library. Virtual screening shows the importance of active site and hinge region residue for interaction with KDR inhibitors. Remarkably the retrieved hits contain a urea backbone, implicating urea derivatives as promising candidate for designing KDR inhibitors. The hydrophobicity of active site, which has until now been overlooked, has been raised into the picture by this study. This can impact on KDR drug development. The study thus quantifies crucial structural requirements necessary for a favourable interaction with the receptor binding site while the cooperative pattern provides important structural clues to chemists for framing potent medicinal agents in future.
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Affiliation(s)
- R K Kar
- Biomedical Informatics Centre, Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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Bhunia GS, Dikhit MR, Kesari S, Sahoo GC, Das P. Corrigendum to "Role of remote sensing, geographic bioinformatics system and bioinformatics in kala-azar epidemiology" [originally published as J Biomed Res 2011, 25(6):373-384; doi:10.1016/S1674-8301(11)60050-X]. J Biomed Res 2012; 26:371. [PMID: 23554773 PMCID: PMC3613733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kumar Kar R, Suryadevara P, Roushan R, Chandra Sahoo G, Ranjan Dikhit M, Das P. Quantifying the Structural Requirements for Designing Newer FLT3 Inhibitors. Med Chem 2012; 8:913-27. [DOI: 10.2174/157340612802084153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 03/07/2012] [Accepted: 03/10/2012] [Indexed: 11/22/2022]
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Sahoo GC, Dikhit MR, Rani M, Ansari MY, Jha C, Rana S, Das P. Analysis of sequence, structure of GAPDH of Leishmania donovani and its interactions. J Biomol Struct Dyn 2012; 31:258-75. [PMID: 22830998 DOI: 10.1080/07391102.2012.698189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Drug resistance acquired by Leishmania donovani (Ldv) is a major problem in the treatment and control of visceral leishmaniasis (VL). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a major glycolytic enzyme has been targeted as is found in other protozoan which cause diseases like sleeping sickness. GAPDH gene of Ldv (AG83 strain) was amplified, sequenced, and modeled on the basis of crystal structure of Leishmania mexicana. The model of the Ldv GAPDH exhibited NAD-binding domain with Rossmann folding. Virtual screening of different experimentally proved compounds with the crystal and the modeled structures of GAPDH of Leishmania strains revealed diverse binding affinities of different compounds. Comparison of binding affinities (based on different programs) of compounds revealed that discovery studio v2.5 (Ligandfit) was able to predict the most hit compounds, the best hit compounds against GAPDH of Leishmania strains are hydrazine, vetrazine, and benzyl carbazate. It is predicted that patients suffering from both VL and cardiac disorders (atrial fibrillation) may benefit if they are treated with warfarin in conjunction with first-line antileishmanial therapies such as miltefosine and AmBisome.
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Affiliation(s)
- Ganesh Chandra Sahoo
- BioMedical Informatics Center, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, 800007 Patna, India.
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Ansari MY, Dikhit MR, Sahoo GC, Das P. Comparative modeling of HGPRT enzyme of L. donovani and binding affinities of different analogs of GMP. Int J Biol Macromol 2012; 50:637-49. [PMID: 22327112 DOI: 10.1016/j.ijbiomac.2012.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 01/05/2012] [Accepted: 01/10/2012] [Indexed: 11/28/2022]
Abstract
Hypoxanthine-guanine phosphoribosyl transferase (HGPRT; EC 2.4.2.8) is a central enzyme in the purine recycling pathway. Parasitic protozoa (Leishmania donovani) cannot synthesize purines de novo and utilize the salvage pathway to produce purine bases. Thus, this enzyme is targeted in drug discovery and development. The model of the monomeric L. donovani HGPRT showed that this enzyme is an α/β type protein with a PRTase type I folding pattern. Among all of the computationally screened compounds, pentamidine, 1,3-dinitroadamantane, acyclovir and analogs of acyclovir had higher binding affinities than the real substrate (guanosine monophosphate). Amino acids of HGPRT that are frequently involved in the binding of these compounds are Lys 66, Asp 74, Arg 77, Asp 81, Val 88, Tyr 182, Arg 192 and Arg 194. It is predicted that patients suffering from both HIV and visceral leishmaniasis (VL) may benefit if they are treated with acyclovir or pentamidine in conjunction with first-line antileishmanial therapies such as miltefosine and AmBisome.
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Affiliation(s)
- Md Yousuf Ansari
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
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Bhunia GS, Dikhit MR, Kesari S, Sahoo GC, Das P. Role of remote sensing, geographical information system (GIS) and bioinformatics in kala-azar epidemiology. J Biomed Res 2011; 25:373-84. [PMID: 23554714 PMCID: PMC3596716 DOI: 10.1016/s1674-8301(11)60050-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/21/2011] [Accepted: 09/08/2011] [Indexed: 11/18/2022] Open
Abstract
Visceral leishmaniasis or kala-azar is a potent parasitic infection causing death of thousands of people each year. Medicinal compounds currently available for the treatment of kala-azar have serious side effects and decreased efficacy owing to the emergence of resistant strains. The type of immune reaction is also to be considered in patients infected with Leishmania donovani (L. donovani). For complete eradication of this disease, a high level modern research is currently being applied both at the molecular level as well as at the field level. The computational approaches like remote sensing, geographical information system (GIS) and bioinformatics are the key resources for the detection and distribution of vectors, patterns, ecological and environmental factors and genomic and proteomic analysis. Novel approaches like GIS and bioinformatics have been more appropriately utilized in determining the cause of visearal leishmaniasis and in designing strategies for preventing the disease from spreading from one region to another.
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Affiliation(s)
| | | | - Shreekant Kesari
- *Corresponding authors: Shreekant Kesari, Ph.D, Scientist “C”, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Agamkuan, Patna, Bihar 800007, India. Tel: +91-0612-2636651, E-mail: . Ganesh Chandra Sahoo, Ph.D, Scientist ‘C’, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Agamkuan, Patna, Bihar 800007, India. Tel: +919973935036, E-mail:
| | - Ganesh Chandra Sahoo
- *Corresponding authors: Shreekant Kesari, Ph.D, Scientist “C”, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Agamkuan, Patna, Bihar 800007, India. Tel: +91-0612-2636651, E-mail: . Ganesh Chandra Sahoo, Ph.D, Scientist ‘C’, Rajendra Memorial Research Institute of Medical Sciences (ICMR), Agamkuan, Patna, Bihar 800007, India. Tel: +919973935036, E-mail:
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Dikhit MR, Nathasharma YP, Patel L, Rana SP, Sahoo GC, Das P. A comparative protein function analysis databaseof different Leishmania strains. Bioinformation 2011; 6:20-2. [PMID: 21464840 PMCID: PMC3064847 DOI: 10.6026/97320630006020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 08/26/2010] [Indexed: 12/12/2022] Open
Abstract
A complete understanding of different protein functional families and template information opens new avenues for novel drug development. Protein identification and analysis software performs a central role in the investigation of proteins and leads to the development of refined database for description of proteins of different Leishmania strains. There are certain databases for different strains that lack template information and functional family annotation. Rajendra Memorial Research Institute of Medical Sciences (RMRIMS) has developed a web-based unique database to provide information about functional families of different proteins and its template information in different Leishmania species. Based on the template information users can model the tertiary structure of protein. The database facilitates significant relationship between template information and possible protein functional families assigned to different proteins by SVMProt. This database is designed to provide comprehensive descriptions of certain important proteins found in four different species of Leishmania i.e. L. donovani, L. infantum, L. major and L. braziliensis. A specific characterization information table provides information related to species and specific functional families. This database aims to be a resource for scientists working on proteomics. The database is freely available at http://biomedinformri.org/calp/.
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Affiliation(s)
- Manas Ranjan Dikhit
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam kuan, Patna-800007, India
| | - Yangya Prasad Nathasharma
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam kuan, Patna-800007, India
| | - Lelin Patel
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam kuan, Patna-800007, India
| | - Sindhu Prava Rana
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam kuan, Patna-800007, India
| | - Ganesh Chandra Sahoo
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam kuan, Patna-800007, India
| | - Pradeep Das
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Agam kuan, Patna-800007, India
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Abstract
UNLABELLED Databases containing proteomic information have become indispensable for virology studies. As the gap between the amount of sequence information and functional characterization widens, increasing efforts are being directed to the development of databases. For virologist, it is therefore desirable to have a single data collection point which integrates research related data from different domains. CHPVDB is our effort to provide virologist such a one-step information center. We describe herein the creation of CHPVDB, a new database that integrates information of different proteins in to a single resource. For basic curation of protein information, the database relies on features from other selected databases, servers and published reports. This database facilitates significant relationship between molecular analysis, cleavage sites, possible protein functional families assigned to different proteins of Chandipura virus (CHPV) by SVMProt and related tools. AVAILABILITY The database is freely available at http://chpvdb.biomedinformri.org/.
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Affiliation(s)
- Manas Ranjan Dikhit
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India - 800007
| | - Sindhu Prava Rana
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India - 800007
| | - Pradeep Das
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India - 800007
| | - Ganesh Chandra Sahoo
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India - 800007
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Abstract
Identification of different protein functions facilitates a mechanistic understanding of Japanese encephalitis virus (JEV) infection and opens novel means for drug development. Support vector machines (SVM), useful for predicting the functional class of distantly related proteins, is employed to ascribe a possible functional class to Japanese encephalitis virus protein. Our study from SVMProt and available JE virus sequences suggests that structural and nonstructural proteins of JEV genome possibly belong to diverse protein functions, are expected to occur in the life cycle of JE virus. Protein functions common to both structural and non-structural proteins are iron-binding, metal-binding, lipid-binding, copper-binding, transmembrane, outer membrane, channels/Pores - Pore-forming toxins (proteins and peptides) group of proteins. Non-structural proteins perform functions like actin binding, zinc-binding, calcium-binding, hydrolases, Carbon-Oxygen Lyases, P-type ATPase, proteins belonging to major facilitator family (MFS), secreting main terminal branch (MTB) family, phosphotransfer-driven group translocators and ATP-binding cassette (ABC) family group of proteins. Whereas structural proteins besides belonging to same structural group of proteins (capsid, structural, envelope), they also perform functions like nuclear receptor, antibiotic resistance, RNA-binding, DNA-binding, magnesium-binding, isomerase (intra-molecular), oxidoreductase and participate in type II (general) secretory pathway (IISP).
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Affiliation(s)
- Ganesh Chandra Sahoo
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna-800007, India.
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