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Article ; Online: An integrated virtual screening of compounds from

Hariyono, Pandu / Patramurti, Christine / Candrasari, Damiana S / Hariono, Maywan

Results in chemistry

2021 Volume 3, Page(s) 100113

Abstract: The pandemic of SARS-Coronavirus-2 (Coronavirus-19) has been progressing by the increasing trend of the cases as well as deaths with neither vaccine nor drug is rationally used to stop the viral spread over. This study aims to perform an integrated ... ...

Abstract	The pandemic of SARS-Coronavirus-2 (Coronavirus-19) has been progressing by the increasing trend of the cases as well as deaths with neither vaccine nor drug is rationally used to stop the viral spread over. This study aims to perform an integrated virtual screening of compounds that had been identified from
Language	English
Publishing date	2021-02-18
Publishing country	Netherlands
Document type	Journal Article
ISSN	2211-7156
ISSN (online)	2211-7156
DOI	10.1016/j.rechem.2021.100113
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: 2-Phenoxyacetamide derivatives as SARS-CoV-2 main protease inhibitor: In silico studies.

Hariyono, Pandu / Dwiastuti, Rini / Yusuf, Muhammad / Salin, Nurul H / Hariono, Maywan

Results in chemistry

2021 Volume 4, Page(s) 100263

Abstract: 2-Phenoxyacetamide group has been identified as one of markers in the discovery and development of SARS-CoV-2 antiviral agent through its main protease ( ... ...

Abstract	2-Phenoxyacetamide group has been identified as one of markers in the discovery and development of SARS-CoV-2 antiviral agent through its main protease (M
Language	English
Publishing date	2021-12-12
Publishing country	Netherlands
Document type	Journal Article
ISSN	2211-7156
ISSN (online)	2211-7156
DOI	10.1016/j.rechem.2021.100263
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: An integrated virtual screening of compounds from Carica papaya leaves against multiple protein targets of SARS-Coronavirus-2

Pandu Hariyono / Christine Patramurti / Damiana S. Candrasari / Maywan Hariono

Results in Chemistry, Vol 3, Iss , Pp 100113- (2021)

2021

Abstract	The pandemic of SARS-Coronavirus-2 (Coronavirus-19) has been progressing by the increasing trend of the cases as well as deaths with neither vaccine nor drug is rationally used to stop the viral spread over. This study aims to perform an integrated virtual screening of compounds that had been identified from Carica papaya leaves, which are proposed to be a herbal treatment for SARS-Coronavirus-2. The screening was initiated by evaluating the 40 compounds from Carica papaya leaves for their drug-like likeness property. The selected compounds were then secondly screened using carcinogenic and toxicity filters. Further selected compounds were thirdly screened for their pharmacokinetic profile and the screening was lastly performed by docking the third selected compounds against multiple protein targets of SARS-Coronavirus-2 employing 3-chymotrypsin-like protease (3CLpro), papain-like protease (PLpro), RNA-dependent-RNA-polymerase (RdRp), endonuclease (EndoU), S1 and S2 region of spike protein. The results show that 20 of 40 compounds, which meet the requirements of drug-like likeness, carcinogenicity-toxicity filter, and pharmacokinetic profiles, can interact with the multiple protein targets of SARS-Coronavirus-2 with the order from high to low affinity as follows: S1 > 3CLpro > EndoU > RdRp > PLpro > S2. In conclusion, Carica papaya leaves are worth to be proposed for further in vitro study against SARS-Coronavirus-2 at both molecular and cellular levels.
Keywords	ADMET prediction ; Carica papaya ; Coronavirus ; COVID-19 ; Natural product ; Virtual screening ; Chemistry ; QD1-999
Subject code	540 ; 500
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: 2-Phenoxyacetamide derivatives as SARS-CoV-2 main protease inhibitor

Pandu Hariyono / Rini Dwiastuti / Muhammad Yusuf / Nurul H. Salin / Maywan Hariono

Results in Chemistry, Vol 4, Iss , Pp 100263- (2022)

In silico studies

2022

Abstract: 2-Phenoxyacetamide group has been identified as one of markers in the discovery and development of SARS-CoV-2 antiviral agent through its main protease (Mpro) inhibition pathway. This study aims to study a series of 2-phenoxyacetamide derivatives using ... ...

Abstract	2-Phenoxyacetamide group has been identified as one of markers in the discovery and development of SARS-CoV-2 antiviral agent through its main protease (Mpro) inhibition pathway. This study aims to study a series of 2-phenoxyacetamide derivatives using in silico method toward SARS-CoV-2 Mpro as the protein target. The study was initiated by employing structure-based pharmacophore to virtually screen and to select the ligands, which have the best fit score (hits) along with the common pharmacophore features being matched. The result shows that from the 11 ligands designed, four ligands are selected as the hits by demonstrating fit score in the range of 56.20 to 65.53 to the pharmacophore model, employing hydrogen bond acceptor (HBA) and hydrophobic (H) as the common features. The hits were then docked into the binding site of the Mpro to see the binding mode of the corresponding hits as well as its affinity. The docking results free energy of binding (ΔGbind) of the hits are in agreement with the pharmacophore fit score, in the range of −6.83 to −7.20 kcal/ mol. To gain the information of the hits as a potential drug to be developed, the in silico study was further proceed by predicting the mutagenic potency, toxicity and pharmacokinetic profiles. Based on the efficiency percentage, all hits meet the criteria as drug candidates by showing 84–88% leading to a conclusion that 2-phenoxyacetamide derivatives are beneficial to be marked as the lead compound for SARS-CoV-2 Mpro inhibitor.
Keywords	2-Phenoxyacetamide ; SARS-CoV-2 ; Main protease ; In silico ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Potential SARS-CoV-2 3CLpro inhibitors from chromene, flavonoid and hydroxamic acid compound based on FRET assay, docking and pharmacophore studies.

Hariono, Maywan / Hariyono, Pandu / Dwiastuti, Rini / Setyani, Wahyuning / Yusuf, Muhammad / Salin, Nurul / Wahab, Habibah

Results in chemistry

2021 Volume 3, Page(s) 100195

Abstract: This present study reports some natural products and one hydroxamic acid synthetic compound which were previously reported as matrix metalloproteinase-9 (MMP-9) inhibitors to be evaluated for their inhibition toward severe acute respiratory syndrome ... ...

Abstract	This present study reports some natural products and one hydroxamic acid synthetic compound which were previously reported as matrix metalloproteinase-9 (MMP-9) inhibitors to be evaluated for their inhibition toward severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) 3-chymotrypsin-like protease (3CLpro). This enzyme is one of the proteins responsible for this coronaviral replication. Two herbal methanolic extracts i.e.,
Language	English
Publishing date	2021-09-20
Publishing country	Netherlands
Document type	Journal Article
ISSN	2211-7156
ISSN (online)	2211-7156
DOI	10.1016/j.rechem.2021.100195
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Future of

Hariono, Maywan / Julianus, Jeffry / Djunarko, Ipang / Hidayat, Irwan / Adelya, Lintang / Indayani, Friska / Auw, Zerlinda / Namba, Gabriel / Hariyono, Pandu

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 22

Abstract: ... Carica ... ...

Abstract	Carica papaya
MeSH term(s)	Carica/chemistry ; Chikungunya Fever/drug therapy ; Dengue/drug therapy ; Herbal Medicine ; Humans ; Malaria/drug therapy ; Plant Extracts/chemistry ; Plant Extracts/therapeutic use ; Plant Leaves/chemistry
Chemical Substances	Plant Extracts
Language	English
Publishing date	2021-11-17
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26226922
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Article: A study on catalytic and non-catalytic sites of H5N1 and H1N1 neuraminidase as the target for chalcone inhibitors

Hariyono, Pandu / Kotta, Jasvidianto Chriza / Adhipandito, Christophorus Fideluno / Aprilianto, Eko / Candaya, Evan Julian / Wahab, Habibah A. / Hariono, Maywan

Applied biological chemistry. 2021 Dec., v. 64, no. 1

2021

Abstract: The H1N1 pandemic in 2009 and the H5N1 outbreak in 2005 have shocked the world as millions of people were infected and hundreds of thousands died due to the infections by the influenza virus. Oseltamivir, the most common drug to block the viral life ... ...

Abstract	The H1N1 pandemic in 2009 and the H5N1 outbreak in 2005 have shocked the world as millions of people were infected and hundreds of thousands died due to the infections by the influenza virus. Oseltamivir, the most common drug to block the viral life cycle by inhibiting neuraminidase (NA) enzyme, has been less effective in some resistant cases due to the virus mutation. Presently, the binding of 10 chalcone derivatives towards H5N1 and H1N1 NAs in the non-catalytic and catalytic sites was studied using molecular docking. The in silico study was also conducted for its drug-like likeness such as Lipinski Rule, mutagenicity, toxicity and pharmacokinetic profiles. The result demonstrates that two chalcones (1c and 2b) have the potential for future NA inhibitor development. Compound 1c inhibits H5N1 NA and H1N1 NA with IC₅₀ of 27.63 µM and 28.11 µM, respectively, whereas compound 2b inhibits NAs with IC₅₀ of 87.54 µM and 73.17 µM for H5N1 and H1N1, respectively. The in silico drug-like likeness prediction reveals that 1c is 62% better than 2b (58%) in meeting the criteria. The results suggested that 1c and 2b have potencies to be developed as non-competitive inhibitors of neuraminidase for the future development of anti-influenza drugs.
Keywords	Orthomyxoviridae ; chalcone ; computer simulation ; drugs ; mutagenicity ; mutation ; oseltamivir ; pandemic ; pharmacokinetics ; prediction ; sialidase ; viruses
Language	English
Dates of publication	2021-12
Size	p. 69.
Publishing place	Springer Singapore
Document type	Article
ZDB-ID	2846955-0
ISSN	2468-0842 ; 2468-0834
ISSN (online)	2468-0842
ISSN	2468-0834
DOI	10.1186/s13765-021-00639-w
Database	NAL-Catalogue (AGRICOLA)

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Article: A study on catalytic and non-catalytic sites of H5N1 and H1N1 neuraminidase as the target for chalcone inhibitors.

Hariyono, Pandu / Kotta, Jasvidianto Chriza / Adhipandito, Christophorus Fideluno / Aprilianto, Eko / Candaya, Evan Julian / Wahab, Habibah A / Hariono, Maywan

Applied biological chemistry

2021 Volume 64, Issue 1, Page(s) 69

Abstract	The H1N1 pandemic in 2009 and the H5N1 outbreak in 2005 have shocked the world as millions of people were infected and hundreds of thousands died due to the infections by the influenza virus. Oseltamivir, the most common drug to block the viral life cycle by inhibiting neuraminidase (NA) enzyme, has been less effective in some resistant cases due to the virus mutation. Presently, the binding of 10 chalcone derivatives towards H5N1 and H1N1 NAs in the non-catalytic and catalytic sites was studied using molecular docking. The in silico study was also conducted for its drug-like likeness such as Lipinski Rule, mutagenicity, toxicity and pharmacokinetic profiles. The result demonstrates that two chalcones ( Supplementary information: The online version contains supplementary material available at 10.1186/s13765-021-00639-w.
Language	English
Publishing date	2021-09-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2846955-0
ISSN	2468-0842 ; 2468-0834
ISSN (online)	2468-0842
ISSN	2468-0834
DOI	10.1186/s13765-021-00639-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Bioguided Fractionation of Local Plants against Matrix Metalloproteinase9 and Its Cytotoxicity against Breast Cancer Cell Models: In Silico and In Vitro Study (Part II).

Hariono, Maywan / Rollando, Rollando / Yoga, I / Harjono, Abraham / Suryodanindro, Alfonsus / Yanuar, Michael / Gonzaga, Thomas / Parabang, Zet / Hariyono, Pandu / Febriansah, Rifki / Hermawansyah, Adi / Setyani, Wahyuning / Wahab, Habibah

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 5

Abstract: In our previous work, the partitions (1 mg/mL) ... ...

Abstract	In our previous work, the partitions (1 mg/mL) of
MeSH term(s)	Ageratum/metabolism ; Antineoplastic Agents, Phytogenic/pharmacology ; Breast Neoplasms/metabolism ; Cell Line, Tumor ; Chemical Fractionation ; Diethylhexyl Phthalate/chemistry ; Diethylhexyl Phthalate/isolation & purification ; Hexanes ; Humans ; Matrix Metalloproteinase 9/metabolism ; Matrix Metalloproteinase 9/physiology ; Matrix Metalloproteinase Inhibitors/pharmacology ; Molecular Docking Simulation ; Oxytetracycline/chemistry ; Oxytetracycline/isolation & purification ; Plant Extracts/pharmacology ; Plant Leaves/drug effects ; Rubiaceae/metabolism
Chemical Substances	Antineoplastic Agents, Phytogenic ; Hexanes ; Matrix Metalloproteinase Inhibitors ; Plant Extracts ; n-hexane (2DDG612ED8) ; Diethylhexyl Phthalate (C42K0PH13C) ; Matrix Metalloproteinase 9 (EC 3.4.24.35) ; Oxytetracycline (X20I9EN955)
Language	English
Publishing date	2021-03-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26051464
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Bioguided Fractionation of Local Plants against Matrix Metalloproteinase9 and Its Cytotoxicity against Breast Cancer Cell Models

Maywan Hariono / Rollando Rollando / I Yoga / Abraham Harjono / Alfonsus Suryodanindro / Michael Yanuar / Thomas Gonzaga / Zet Parabang / Pandu Hariyono / Rifki Febriansah / Adi Hermawansyah / Wahyuning Setyani / Habibah Wahab

Molecules, Vol 26, Iss 1464, p

In Silico and In Vitro Study (Part II)

2021 Volume 1464

Abstract: In our previous work, the partitions (1 mg/mL) of Ageratum conyzoides (AC) aerial parts and Ixora coccinea (IC) leaves showed inhibitions of 94% and 96%, respectively, whereas their fractions showed IC 50 43 and 116 µg/mL, respectively, toward Matrix ... ...

Abstract	In our previous work, the partitions (1 mg/mL) of Ageratum conyzoides (AC) aerial parts and Ixora coccinea (IC) leaves showed inhibitions of 94% and 96%, respectively, whereas their fractions showed IC 50 43 and 116 µg/mL, respectively, toward Matrix Metalloproteinase9 (MMP9), an enzyme that catalyzes a proteolysis of extracellular matrix. In this present study, we performed IC 50 determinations for AC n -hexane, IC n -hexane, and IC ethylacetate partitions, followed by the cytotoxicity study of individual partitions against MDA-MB-231, 4T1, T47D, MCF7, and Vero cell lines. Successive fractionations from AC n -hexane and IC ethylacetate partitions led to the isolation of two compounds, oxytetracycline (OTC) and dioctyl phthalate (DOP). The result showed that AC n -hexane, IC n -hexane, and IC ethylacetate partitions inhibit MMP9 with their respective IC 50 as follows: 246.1 µg/mL, 5.66 µg/mL, and 2.75 × 10 −2 µg/mL. Toward MDA-MB-231, 4T1, T47D, and MCF7, AC n -hexane demonstrated IC 50 2.05, 265, 109.70, and 2.11 µg/mL, respectively, whereas IC ethylacetate showed IC 50 1.92, 57.5, 371.5, and 2.01 µg/mL, respectively. The inhibitions toward MMP9 by OTC were indicated by its IC 50 18.69 µM, whereas DOP was inactive. A molecular docking study suggested that OTC prefers to bind to PEX9 rather than its catalytic domain. Against 4T1, OTC showed inhibition with IC 50 414.20 µM. In conclusion, this study furtherly supports the previous finding that AC and IC are two herbals with potential to be developed as triple-negative anti-breast cancer agents.
Keywords	MMP9 ; PEX9 ; cancer ; bioguided ; fractionation ; ageratum ; Organic chemistry ; QD241-441
Subject code	580
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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