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Article ; Online: Antiparasitic effect of Farnesol against Leishmania major

Harshita Sharma / Rakesh Sehgal / Nishant Shekhar / Gaurav Shoeran / Upninder Kaur / Bikash Medhi

PLoS ONE, Vol 18, Iss

A rationale from in vitro and in silico investigations

2023 Volume 11

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Antiparasitic effect of Farnesol against Leishmania major: A rationale from in vitro and in silico investigations.

Sharma, Harshita / Sehgal, Rakesh / Shekhar, Nishant / Shoeran, Gaurav / Kaur, Upninder / Medhi, Bikash

PloS one

2023 Volume 18, Issue 11, Page(s) e0293290

Abstract: Leishmaniasis is a vector-borne parasitic infection caused by the infective bite of female Phlebotomine sandflies. Treatment of leishmaniasis by conventional synthetic compounds is met by challenges pertaining to adverse effects which call for the ... ...

Abstract	Leishmaniasis is a vector-borne parasitic infection caused by the infective bite of female Phlebotomine sandflies. Treatment of leishmaniasis by conventional synthetic compounds is met by challenges pertaining to adverse effects which call for the discovery of newer anti-leishmanial molecules. This study was performed to evaluate the effect and modes of action of a sesquiterpene alcoholic molecule Farnesol on Leishmania major, the causative agent of Zoonotic CL. The cytotoxic effect of Farnesol against L.major promastigotes, amastigotes and macrophages was assessed by MTT test and counting. The IC50 on promastigotes by Farnesol on L.major was also evaluated by flow cytometry. In the findings, promastigotes were reduced at 167μM. The mean numbers of L.major amastigotes in macrophages were significantly decreased on exposure to Farnesol at 172μM. In addition, Farnesol induced significant apoptosis dose-dependent on L.major promastigotes. In silico protein-ligand_binding analyses indicated the effect of Farnesol in perturbation of the ergosterol synthesis pathway of Leishmania with attributes suggesting inhibition of Lanosterol-α-demethylase, the terminal enzyme of ergosterol synthesis machinery. Findings from flow cytometry reveal the role of Farnesol in apoptosis-induced killing in promastigotes. Farnesol was effective at very lower concentrations when compared to Paromomycin. Further studies are crucial to evaluate the therapeutic potential of Farnesol alone or in combination with other conventional drugs in animal models.
MeSH term(s)	Animals ; Female ; Antiparasitic Agents/pharmacology ; Leishmania major ; Farnesol/pharmacology ; Anti-Infective Agents/pharmacology ; Leishmaniasis/drug therapy ; Ergosterol/pharmacology ; Antiprotozoal Agents/pharmacology
Chemical Substances	Antiparasitic Agents ; Farnesol (4602-84-0) ; Anti-Infective Agents ; Ergosterol (Z30RAY509F) ; Antiprotozoal Agents
Language	English
Publishing date	2023-11-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0293290
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: In-silico discovery of dual active molecule to restore synaptic wiring against autism spectrum disorder via HDAC2 and H3R inhibition.

Raja, Anupam / Shekhar, Nishant / Singh, Harvinder / Prakash, Ajay / Medhi, Bikash

PloS one

2022 Volume 17, Issue 7, Page(s) e0268139

Abstract: Metal-dependent histone deacetylases (HDACs) are essential epigenetic regulators; their molecular and pharmacological roles in medically critical diseases such as neuropsychiatric disorders, neurodegeneration, and cancer are being studied globally. HDAC2' ...

Abstract	Metal-dependent histone deacetylases (HDACs) are essential epigenetic regulators; their molecular and pharmacological roles in medically critical diseases such as neuropsychiatric disorders, neurodegeneration, and cancer are being studied globally. HDAC2's differential expression in the central nervous system makes it an appealing therapeutic target for chronic neurological diseases like autism spectrum disorder. In this study, we identified H3R inhibitor molecules that are computationally effective at binding to the HDAC2 metal-coordinated binding site. The study highlights the importance of pitolisant in screening the potential H3R inhibitors by using a hybrid workflow of ligand and receptor-based drug discovery. The screened lead compounds with PubChem SIDs 103179850, 103185945, and 103362074 show viable binding with HDAC2 in silico. The importance of ligand contacts with the Zn2+ ion in the HDAC2 catalytic site is also discussed and investigated for a significant role in enzyme inhibition. The proposed H3R inhibitors 103179850, 103185945, and 103362074 are estimated as dual-active molecules to block the HDAC2-mediated deacetylation of the EAAT2 gene (SLC1A2) and H3R-mediated synaptic transmission irregularity and are, therefore, open for experimental validation.
MeSH term(s)	Autism Spectrum Disorder/drug therapy ; Autism Spectrum Disorder/genetics ; Histone Deacetylase 2/genetics ; Histone Deacetylase 2/metabolism ; Histone Deacetylase Inhibitors/chemistry ; Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylases/metabolism ; Humans ; Ligands ; Synaptic Transmission
Chemical Substances	Histone Deacetylase Inhibitors ; Ligands ; HDAC2 protein, human (EC 3.5.1.98) ; Histone Deacetylase 2 (EC 3.5.1.98) ; Histone Deacetylases (EC 3.5.1.98)
Language	English
Publishing date	2022-07-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0268139
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Article ; Online: Antiparasitic effect of Farnesol against Leishmania major

Harshita Sharma / Rakesh Sehgal / Nishant Shekhar / Gaurav Shoeran / Upninder Kaur / Bikash Medhi

PLoS ONE, Vol 18, Iss 11, p e

A rationale from in vitro and in silico investigations.

2023 Volume 0293290

Abstract	Leishmaniasis is a vector-borne parasitic infection caused by the infective bite of female Phlebotomine sandflies. Treatment of leishmaniasis by conventional synthetic compounds is met by challenges pertaining to adverse effects which call for the discovery of newer anti-leishmanial molecules. This study was performed to evaluate the effect and modes of action of a sesquiterpene alcoholic molecule Farnesol on Leishmania major, the causative agent of Zoonotic CL. The cytotoxic effect of Farnesol against L.major promastigotes, amastigotes and macrophages was assessed by MTT test and counting. The IC50 on promastigotes by Farnesol on L.major was also evaluated by flow cytometry. In the findings, promastigotes were reduced at 167μM. The mean numbers of L.major amastigotes in macrophages were significantly decreased on exposure to Farnesol at 172μM. In addition, Farnesol induced significant apoptosis dose-dependent on L.major promastigotes. In silico protein-ligand_binding analyses indicated the effect of Farnesol in perturbation of the ergosterol synthesis pathway of Leishmania with attributes suggesting inhibition of Lanosterol-α-demethylase, the terminal enzyme of ergosterol synthesis machinery. Findings from flow cytometry reveal the role of Farnesol in apoptosis-induced killing in promastigotes. Farnesol was effective at very lower concentrations when compared to Paromomycin. Further studies are crucial to evaluate the therapeutic potential of Farnesol alone or in combination with other conventional drugs in animal models.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: In-silico discovery of dual active molecule to restore synaptic wiring against autism spectrum disorder via HDAC2 and H3R inhibition.

Anupam Raja / Nishant Shekhar / Harvinder Singh / Ajay Prakash / Bikash Medhi

PLoS ONE, Vol 17, Iss 7, p e

2022 Volume 0268139

Abstract	Metal-dependent histone deacetylases (HDACs) are essential epigenetic regulators; their molecular and pharmacological roles in medically critical diseases such as neuropsychiatric disorders, neurodegeneration, and cancer are being studied globally. HDAC2's differential expression in the central nervous system makes it an appealing therapeutic target for chronic neurological diseases like autism spectrum disorder. In this study, we identified H3R inhibitor molecules that are computationally effective at binding to the HDAC2 metal-coordinated binding site. The study highlights the importance of pitolisant in screening the potential H3R inhibitors by using a hybrid workflow of ligand and receptor-based drug discovery. The screened lead compounds with PubChem SIDs 103179850, 103185945, and 103362074 show viable binding with HDAC2 in silico. The importance of ligand contacts with the Zn2+ ion in the HDAC2 catalytic site is also discussed and investigated for a significant role in enzyme inhibition. The proposed H3R inhibitors 103179850, 103185945, and 103362074 are estimated as dual-active molecules to block the HDAC2-mediated deacetylation of the EAAT2 gene (SLC1A2) and H3R-mediated synaptic transmission irregularity and are, therefore, open for experimental validation.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Computational attributes of protein kinase-C gamma C2-domain & virtual screening for small molecules: elucidation from meta-dynamics simulations & free-energy calculations.

Singh, Harvinder / Raja, Anupam / Shekhar, Nishant / Chauhan, Arushi / Prakash, Ajay / Avti, Pramod / Medhi, Bikash

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 11, Page(s) 4981–4992

Abstract: Epilepsy, a moderate to chronic neuropathological condition, is induced by the acute blockage of synaptic and voltage-gated inhibitory conduction or through the activation of synaptic and voltage-gated excitatory conduction. The regulation of long-term ... ...

Abstract	Epilepsy, a moderate to chronic neuropathological condition, is induced by the acute blockage of synaptic and voltage-gated inhibitory conduction or through the activation of synaptic and voltage-gated excitatory conduction. The regulation of long-term potentiation (LTP) is important in the regulation of epileptic events, and its activity is linked to specific protein kinases. The PKC-γ subtype is a vaguely explored therapeutic target for neurological disorders, but in selected studies, it is proven to be a critical intermediate protein in LTP. This study utilized computational modelling approaches including receptor-based docking, QSAR followed by explicit binding score assessment method MM/GBSA, MM/PBSA (EDA) and MTD simulation-based FES iteration. This was performed to virtually screen the small molecule libraries, which comprised about 2.79 lacs compounds against the Ca
MeSH term(s)	Molecular Dynamics Simulation ; Binding Sites ; Proteins ; Small Molecule Libraries/chemistry ; Molecular Docking Simulation
Chemical Substances	Proteins ; Small Molecule Libraries
Language	English
Publishing date	2022-05-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2077447
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Article ; Online: Indomethacin: an exploratory study of antiviral mechanism and host-pathogen interaction in COVID-19.

Shekhar, Nishant / Kaur, Harpinder / Sarma, Phulen / Prakash, Ajay / Medhi, Bikash

Expert review of anti-infective therapy

2021 Volume 20, Issue 3, Page(s) 383–390

Abstract: Introduction: COVID-19, a dreadful pandemic that has impacted human life like no other pathogenic invasion, has claimed the lives of over 100 million people. The need for effective treatment strategies is still a subject of intense research considering ... ...

Abstract	Introduction: COVID-19, a dreadful pandemic that has impacted human life like no other pathogenic invasion, has claimed the lives of over 100 million people. The need for effective treatment strategies is still a subject of intense research considering the rapidly evolving genome and continental diversity. Indomethacin is administered mostly as co-treatment for affected patients as a non-steroidal anti-inflammatory drug (NSAID). However, the underlying mechanism of action is unresolved. This study explores the basal mechanism of indomethacin and potency in alleviating the damage caused by SARS-CoV-2 and discusses the experimental and clinical efficacy in recent studies. Areas covered: The literature search and system biology-based network formation were employed to describe the potent effects and risks associated with indomethacin in in-vitro, in-vivo, and clinical studies. This study also highlights the plausible mechanism of antiviral action of indomethacin with its apparent viral protein targets. The SARS-CoV-2 protein, the interacting host proteins, and the effect of indomethacin on this interactome as a standalone treatment or as part of a co-therapy strategy are particularly emphasized using network modeling. Expert opinion: Indomethacin has demonstrated excellent clinical endpoint characteristics in several studies, and we recommend that it be utilized in the treatment of mild-to-moderate COVID patients.
MeSH term(s)	Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Host-Pathogen Interactions ; Humans ; Indomethacin/pharmacology ; Indomethacin/therapeutic use ; SARS-CoV-2/drug effects
Chemical Substances	Antiviral Agents ; Indomethacin (XXE1CET956)
Language	English
Publishing date	2021-10-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2181279-2
ISSN	1744-8336 ; 1478-7210
ISSN (online)	1744-8336
ISSN	1478-7210
DOI	10.1080/14787210.2022.1990756
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Zs.A 6106: Show issues

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Article: A Retrospective Audit of Demography and Different Surgical Modalities Adopted for Giant Cell Tumor of Bone in Eastern India.

Kumar, Indrajeet / Ahmed, Wasim / Kashyap, Nishant / Kumar, Manish / Saw, Manish K / Shekhar, Ravi

Cureus

2022 Volume 14, Issue 9, Page(s) e29520

Abstract: Background and objective There is scarce data on demography and different surgical treatment modalities for giant cell tumor of bone (GCTB) from eastern India. In light of this, the present study aimed to examine the demographic characteristics, ... ...

Abstract	Background and objective There is scarce data on demography and different surgical treatment modalities for giant cell tumor of bone (GCTB) from eastern India. In light of this, the present study aimed to examine the demographic characteristics, different surgical treatment modalities, and recurrence rate of GCTB at a tertiary care institute in Bihar. Materials and methods A retrospective audit of 52 GCTB patients who were treated at the center from January 2016 to December 2020 was conducted. The minimum follow-up period was one year. GCTB patients underwent surgical procedures ranging from extended intralesional curettage with bone graft or bone cement with or without fixation to wide local excision to resection with or without reconstruction or amputation depending on the stage and site of the tumors. Results The mean age of patients was 31.86 years (range: 13-67 years). The distal femur (20 patients, 38.46%) and proximal tibia (11 patients, 21.15%) were the most common sites of the tumor. Sixty-eight confirmed cases (male: 32, female: 36) of GCTB were operated on, with a male-to-female ratio of 1:1.125. Sixteen patients (four males and 12 females) were lost to follow-up. So, the final study consisted of 52 patients with a median age of 28 years (first quartile: 24 years, third quartile: 38 years). The majority of patients (32 patients, 61.53%) were in the third and fourth decades of life. Conclusion Based on this retrospective audit, it is concluded that the knee region is the most common site of GCTB. Surgery is the mainstay of management. Most of the patients came under Campanacci Grade 3 with low compliance with follow-up and adherence to the treatment. Hence, educational programs, the establishment of early detection centers, and timely referral to expert treatment are necessary.
Language	English
Publishing date	2022-09-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.29520
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Article: Ivermectin as a potential drug for treatment of COVID-19: an in-sync review with clinical and computational attributes.

Kaur, Harpinder / Shekhar, Nishant / Sharma, Saurabh / Sarma, Phulen / Prakash, Ajay / Medhi, Bikash

Pharmacological reports : PR

2021 Volume 73, Issue 3, Page(s) 736–749

Abstract: Introduction: COVID-19 cases are on surge; however, there is no efficient treatment or vaccine that can be used for its management. Numerous clinical trials are being reviewed for use of different drugs, biologics, and vaccines in COVID-19. A much ... ...

Abstract	Introduction: COVID-19 cases are on surge; however, there is no efficient treatment or vaccine that can be used for its management. Numerous clinical trials are being reviewed for use of different drugs, biologics, and vaccines in COVID-19. A much empirical approach will be to repurpose existing drugs for which pharmacokinetic and safety data are available, because this will facilitate the process of drug development. The article discusses the evidence available for the use of Ivermectin, an anti-parasitic drug with antiviral properties, in COVID-19. Methods: A rational review of the drugs was carried out utilizing their clinically significant attributes. A more thorough understanding was met by virtual embodiment of the drug structure and realizable viral targets using artificial intelligence (AI)-based and molecular dynamics (MD)-simulation-based study. Conclusion: Certain studies have highlighted the significance of ivermectin in COVID-19; however, it requires evidences from more Randomised Controlled Trials (RCTs) and dose- response studies to support its use. In silico-based analysis of ivermectin's molecular interaction specificity using AI and classical mechanics simulation-based methods indicates positive interaction of ivermectin with viral protein targets, which is leading for SARS-CoV 2 N-protein NTD (nucleocapsid protein N-terminal domain).
MeSH term(s)	Animals ; Antiparasitic Agents/pharmacology ; Antiparasitic Agents/therapeutic use ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Humans ; Ivermectin/pharmacology ; Ivermectin/therapeutic use ; Molecular Dynamics Simulation
Chemical Substances	Antiparasitic Agents ; Antiviral Agents ; Ivermectin (70288-86-7)
Language	English
Publishing date	2021-01-03
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2186248-5
ISSN	1734-1140
ISSN	1734-1140
DOI	10.1007/s43440-020-00195-y
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Zs.A 861: Show issues

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Article ; Online: Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein-protein interactions.

Kaur, Gurjeet / Prajapat, Manisha / Singh, Harvinder / Sarma, Phulen / Bhadada, Sanjay Kumar / Shekhar, Nishant / Sharma, Saurabh / Sinha, Shweta / Kumar, Subodh / Prakash, Ajay / Medhi, Bikash

Scientific reports

2023 Volume 13, Issue 1, Page(s) 9337

Abstract: Protein-protein interactions (PPIs) play a critical role in all biological processes. Menin is tumor suppressor protein, mutated in multiple endocrine neoplasia type 1 syndrome and has been shown to interact with multiple transcription factors including ( ...

Abstract	Protein-protein interactions (PPIs) play a critical role in all biological processes. Menin is tumor suppressor protein, mutated in multiple endocrine neoplasia type 1 syndrome and has been shown to interact with multiple transcription factors including (RPA2) subunit of replication protein A (RPA). RPA2, heterotrimeric protein required for DNA repair, recombination and replication. However, it's still remains unclear the specific amino acid residues that have been involved in Menin-RPA2 interaction. Thus, accurately predicting the specific amino acid involved in interaction and effects of MEN1 mutations on biological systems is of great interests. The experimental approaches for identifying amino acids in menin-RPA2 interactions are expensive, time-consuming, and challenging. This study leverages computational tools, free energy decomposition and configurational entropy scheme to annotate the menin-RPA2 interaction and effect on menin point mutation, thereby proposing a viable model of menin-RPA2 interaction. The menin-RPA2 interaction pattern was calculated on the basis of different 3D structures of menin and RPA2 complexes, constructed using homology modeling and docking strategy, generating three best-fit models: Model 8 (- 74.89 kJ/mol), Model 28 (- 92.04 kJ/mol) and Model 9 (- 100.4 kJ/mol). The molecular dynamic (MD) was performed for 200 ns and binding free energies and energy decomposition analysis were calculated using Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) in GROMACS. From binding free energy change, model 8 of Menin-RPA2 exhibited most negative binding energy of - 205.624 kJ/mol, followed by model 28 of Menin-RPA2 with - 177.382 kJ/mol. After S606F point mutation in Menin, increase of BFE (ΔG
MeSH term(s)	Humans ; Point Mutation ; Mutation ; Transcription Factors/genetics ; Binding Sites ; Multiple Endocrine Neoplasia Type 1 ; Amino Acids/genetics ; Replication Protein A/genetics
Chemical Substances	Transcription Factors ; Amino Acids ; RPA2 protein, human (EC 2.7.7.7) ; Replication Protein A
Language	English
Publishing date	2023-06-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-35599-2
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