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Article ; Online: The Potential of Clerodendrum paniculatum Leaves Fraction as a 3-Chymotrypsin-Like (3CL) Protease Inhibitor of SARS-CoV-2

Muhammad Arba / Arfan Arfan / Yamin Yamin / Muhammad Sulaiman Zubair

Indonesian Journal of Chemistry, Vol 23, Iss 3, Pp 770-

2023 Volume 781

Abstract: We described the biological activity of the Clerodendrum paniculatum leaf fraction against the SARS-CoV-2 3-Chymotrypsin-like 3CL protease at the molecular level. This study applied LC-MS/MS to identify bioactive compounds from fractions, computational ... ...

Abstract	We described the biological activity of the Clerodendrum paniculatum leaf fraction against the SARS-CoV-2 3-Chymotrypsin-like 3CL protease at the molecular level. This study applied LC-MS/MS to identify bioactive compounds from fractions, computational studies, and fluorescence resonance energy transfer (FRET) assays to ascertain their inhibitory activity. LC-MS/MS analysis of the three samples revealed that sample 1 contained 18 compound peaks. In samples 2 and 3, there were 23 and 25 compounds with different molecular weights, respectively. Docking's study identified that the alkaloids (komarovicine and roemerine) have lower binding energies than other metabolites and standard compounds, with values of -33.47 and -32.63 kJ/mol, respectively. Roemerine demonstrated excellent stability based on dynamic simulation results and confirmed its affinity for 3CL protease predicted by the MM-PBSA approach of -89.44 kJ/mol. The FRET method for testing 3CL protease activity revealed that sample 2 had an enzyme inhibitory activity of 94.3%, which was close to that of GC376 (98.19%). Meanwhile, samples 1 and 3 yielded satisfactory inhibition activity by 89.64% and 85.24%, respectively. The antiviral activity of C. paniculatum leaves was discovered for the first time by inhibiting the 3CL protease SARS-CoV-2, providing an excellent opportunity for its development as an anti-SARS-CoV-2.
Keywords	clerodendrum paniculatum ; covid-19 ; molecular dynamics simulation ; sars-cov-2 ; 3-chymotrypsin-like protease ; Chemistry ; QD1-999
Subject code	540 ; 500
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Department of Chemistry, Universitas Gadjah Mada
Document type	Article ; Online
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Article ; Online: In Vitro and In Silico Studies of Quercetin and Daidzin as Selective Anticancer Agents

Muhammad Sulaiman Zubair / Syariful Anam / Saipul Maulana / Muhammad Arba

Indonesian Journal of Chemistry, Vol 21, Iss 2, Pp 310-

2021 Volume 317

Abstract: Quercetin and daidzin are flavonoid and flavonoid glycoside type compounds that have been found in many plants and nutraceuticals. This study aims to examine the in vitro cytotoxic and selectivity properties of quercetin and daidzin on breast and ... ...

Abstract	Quercetin and daidzin are flavonoid and flavonoid glycoside type compounds that have been found in many plants and nutraceuticals. This study aims to examine the in vitro cytotoxic and selectivity properties of quercetin and daidzin on breast and cervical cancers and to study their molecular interaction and stability on epidermal growth factor receptor tyrosine kinase (EGFR-TK) by applying molecular docking and molecular dynamics (MD) simulations. In vitro anticancer activity was performed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method on breast cancer cell (T47D), cervical cancer cells (HeLa), and Vero normal cells, while molecular docking and MD simulation were done by using AutoDock Vina and Amber18 package software, respectively. Quercetin and daidzin showed potent cytotoxic and high selectivity on both cell lines. Daidzin was found to has a higher IC50 and selectivity index than quercetin. Docking and MD results showed that both compounds prefer to interact with epidermal growth factor receptor tyrosine kinase (EGFR-TK). Daidzin showed better interaction than quercetin with a docking score of -9.6 kcal/mol. Also, daidzin was found more stable than quercetin with low RMSD and RMSF values.
Keywords	quercetin ; daidzin ; t47d ; hela ; docking ; molecular dynamics ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Department of Chemistry, Universitas Gadjah Mada
Document type	Article ; Online
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Article ; Online: GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from

Zubair, Muhammad Sulaiman / Maulana, Saipul / Widodo, Agustinus / Pitopang, Ramadanil / Arba, Muhammad / Hariono, Maywan

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 17

Abstract: This study aims to identify and isolate the secondary metabolites ... ...

Abstract	This study aims to identify and isolate the secondary metabolites of
MeSH term(s)	Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/metabolism ; Coronavirus 3C Proteases/ultrastructure ; Coronavirus Protease Inhibitors/chemistry ; Coronavirus Protease Inhibitors/isolation & purification ; Coronavirus Protease Inhibitors/pharmacology ; Coronavirus Protease Inhibitors/therapeutic use ; Crystallography, X-Ray ; Enzyme Assays ; Gas Chromatography-Mass Spectrometry ; Zingiber officinale/chemistry ; Humans ; Magnetic Resonance Spectroscopy ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Plant Extracts/chemistry ; Plant Extracts/isolation & purification ; Plant Extracts/pharmacology ; Plant Extracts/therapeutic use ; Pyrrolidines/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Structure-Activity Relationship ; Sulfonic Acids/pharmacology ; COVID-19 Drug Treatment
Chemical Substances	Coronavirus Protease Inhibitors ; Plant Extracts ; Pyrrolidines ; Sulfonic Acids ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; GC376 (H1NMJ5XDG5)
Language	English
Publishing date	2021-08-28
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/molecules26175230
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Article: The Search for Cyclooxygenase-2 (COX-2) Inhibitors for the Treatment of Inflammation Disease: An in-silico Study.

Ruslin, Ruslin / Yamin, Yamin / Kasmawati, Henny / Mangrura, Samuel / Kadidae, Laode / Alroem, Armid / Arba, Muhammad

Journal of multidisciplinary healthcare

2022 Volume 15, Page(s) 783–791

Abstract: Purpose: Cyclooxygenase (COX-2) has been validated as a molecular target for treating inflammatory diseases. The present work was performed to identify potential COX-2 inhibitors by employing pharmacophore modeling.: Methods: The pharmacophore ... ...

Abstract	Purpose: Cyclooxygenase (COX-2) has been validated as a molecular target for treating inflammatory diseases. The present work was performed to identify potential COX-2 inhibitors by employing pharmacophore modeling. Methods: The pharmacophore features consisted of seven features, ie, three hydrophobic, one negative ion, and three hydrogen bond acceptors, which were developed based on the structure of COX-2 inhibitor, (R)-naproxen. Results: The pharmacophore model was validated with a Goodness of Hit (GH score) of 0.754 and the values of AUC100% 0.51. Screening against the ZINC database retrieved 1675 hits, while the molecular docking procedure identified four best hit molecules in term of binding orientation and binding energies, ie, Lig_1805/ZINC103584272 (E = -11.03 kcal/mol), Lig_553/ZINC408573132 (E = -10.92 kcal/mol), Lig_680/ZINC103584263 (E = -10.90 kcal/mol), and Lig_2006/ZINC19324645 (E = -10.62 kcal/mol). Conclusion: The interactions of the four hits occurred in the binding site as (R)-naproxen did, and interestingly, their binding affinities were stronger than (R)-naproxen, implying their potential as COX-2 inhibitors.
Language	English
Publishing date	2022-04-12
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2453343-9
ISSN	1178-2390
ISSN	1178-2390
DOI	10.2147/JMDH.S359429
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Article ; Online: PENGUATAN PERAN WARGA MASYARAKAT DALAM MITIGASI DAN ADAPTASI MENGHADAPI WABAH COVID-19 DI KABUPATEN KONAWE

Arba, Muhammad / Budikafa, Muhammad Jefriyanto / Ruslin, Ruslin

JURNAL ANOA; Vol 1, No; 123-128 ; 10.1234/anoa.v1i3

2020 Volume 3, Issue : Edisi Khusus Covid-19

Abstract: Coronavirus Disease 2019 (COVID-19) telah dinyatakan sebagai pandemi dunia oleh WHO (WHO, 2020). Coronavirus adalah zoonosis atau virus yang ditularkan antara hewan dan manusia. Virus dan penyakit ini diketahui berawal di kota Wuhan, Cina sejak Desember ... ...

Abstract	Coronavirus Disease 2019 (COVID-19) telah dinyatakan sebagai pandemi dunia oleh WHO (WHO, 2020). Coronavirus adalah zoonosis atau virus yang ditularkan antara hewan dan manusia. Virus dan penyakit ini diketahui berawal di kota Wuhan, Cina sejak Desember 2019. Per tanggal 13 juli 2020, jumlah kasus penyakit ini mencapai angka 12.552.765 jiwa yang tersebar di 166 negara, termasuk Indonesia. Perkembangan penyakit COVID-19 yang disebabkan virus corona (SARS-CoV-2) demikian meluas dan memakan cukup banyak korban. Menurut data terakhir Kabupaten Konawe per tanggal 13 Juli 2020 yang diperoleh dari https://dinkes.sultraprov.go.id/info-covid-19-sultra terdapat orang tanpa gejala 18 orang, orang dalam pemantauan 1 orang, pasien dalam Pengawasan 1 orang dan pasien konfirmasi positif 15 orang. Angka ini setidaknya untuk sementara ini cukup tinggi dan kemungkinan besar akan terus bertambah dari hari ke hari. Tujuan program pengabdian kepada masyarakat ini adalah membantu pemerintah kecamatan setempat dalam meningkatkan kesadaran masyarakat untuk mencegah dan melawan virus covid-19. Sasaran dari kegiatan KKN tematik ini adalah masyarakat di Kelurahan Puuduria Kecamatan Wonggeduku dan Desa Baruga Kecamatan Wonggeduku Barat Kabupaten Konawe. Program ini dilaksanakan dengan empat program utama yaitu gerakan masyarakat hidup sehat (Germas), perilaku hidup bersih dan sehat (PHBS), gerakan masyarakat menggunakan masker, antiseptik dan desinfektan (Gemad), dan tanaman obat keluarga (Toga). Hasil kegiatan ini adalah peningkatan pemahaman dan keterampilan masyarakat dalam perilaku hidup bersih dan sehat, cara penggunaan masker, antiseptik dan desinfektan yang baik dan benar serta cara pengolahan tanaman obat keluarga sehingga derajat kesehatan masyarakat akan semakin meningkat.
Keywords	Covid-19 ; Konawe ; Germas ; PHBS ; Gemad ; Toga ; covid19
Language	English
Publishing date	2020-08-01
Publisher	JURNAL ANOA
Publishing country	id
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: GC-MS, LC-MS/MS, Docking and Molecular Dynamics Approaches to Identify Potential SARS-CoV-2 3-Chymotrypsin-Like Protease Inhibitors from Zingiber officinale Roscoe

Muhammad Sulaiman Zubair / Saipul Maulana / Agustinus Widodo / Ramadanil Pitopang / Muhammad Arba / Maywan Hariono

Molecules, Vol 26, Iss 5230, p

2021 Volume 5230

Abstract: This study aims to identify and isolate the secondary metabolites of Zingiber officinale using GC-MS, preparative TLC, and LC-MS/MS methods, to evaluate the inhibitory potency on SARS-CoV-2 3 chymotrypsin-like protease enzyme, as well as to study the ... ...

Abstract	This study aims to identify and isolate the secondary metabolites of Zingiber officinale using GC-MS, preparative TLC, and LC-MS/MS methods, to evaluate the inhibitory potency on SARS-CoV-2 3 chymotrypsin-like protease enzyme, as well as to study the molecular interaction and stability by using docking and molecular dynamics simulations. GC-MS analysis suggested for the isolation of terpenoids compounds as major compounds on methanol extract of pseudostems and rhizomes. Isolation and LC-MS/MS analysis identified 5-hydro-7, 8, 2′-trimethoxyflavanone ( 9 ), ( E )-hexadecyl-ferulate ( 1 ), isocyperol ( 2 ), N- isobutyl-(2 E ,4 E )-octadecadienamide ( 3 ), and nootkatone ( 4 ) from the rhizome extract, as well as from the leaves extract with the absence of 9 . Three known steroid compounds, i.e., spinasterone ( 7 ), spinasterol ( 8 ), and 24-methylcholesta-7-en-3 β -on ( 6 ), were further identified from the pseudostem extract. Molecular docking showed that steroids compounds 7 , 8 , and 6 have lower predictive binding energies (MMGBSA) than other metabolites with binding energy of −87.91, −78.11, and −68.80 kcal/mole, respectively. Further characterization on the single isolated compound by NMR showed that 6 was identified and possessed 75% inhibitory activity on SARS-CoV-2 3CL protease enzyme that was slightly different with the positive control GC376 (77%). MD simulations showed the complex stability with compound 6 during 100 ns simulation time.
Keywords	Zingiber officinale ; LC-MS/MS ; Steroids ; 24-Methylcholesta-7-en-3β-on ; 3CL Protease ; SARS-CoV-2 ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: 198 Interaction of porphyrin-anthraquinone hybrids with HSP90: in silico study.

Arba, Muhammad / Tjahjono, Daryono H

Journal of biomolecular structure & dynamics

2015 Volume 33 Suppl 1, Page(s) 130–131

Language	English
Publishing date	2015
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2015.1032835
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Article ; Online: Identification of Phosphatidylinositol 3-kinase δ (PI3Kδ) Inhibitor

Muhammad Arba / Malindo Sufriadin / Daryono Hadi Tjahjono

Indonesian Journal of Chemistry, Vol 20, Iss 5, Pp 1070-

Pharmacophore-based Virtual Screening and Molecular Dynamics Simulation

2020 Volume 1079

Abstract: Phosphatidylinositol 3-kinase δ (PI3Kδ) is a validated drug target for the treatment of cancer. The present study aims to search for new inhibitors of PI3Kδ by employing pharmacophore modelling using LigandScout Advanced 4.3 software. The three hydrogen ... ...

Abstract	Phosphatidylinositol 3-kinase δ (PI3Kδ) is a validated drug target for the treatment of cancer. The present study aims to search for new inhibitors of PI3Kδ by employing pharmacophore modelling using LigandScout Advanced 4.3 software. The three hydrogen bond acceptors and two hydrophobic features were proposed as a pharmacophore model using LASW1976 structure. The model was then validated using the Area Under Curve (AUC) of Receiver Operating Characteristic (ROC) and GH score. It was used to screen new molecules in the ZINC database, which resulted in 599 hits. All 599 hits were then docked into PI3Kδ protein, and five best hits were submitted to 50 ns molecular dynamics simulations. Each hit complexed with PI3Kδ underwent minor conformational changes as indicated by the values of Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF). Furthermore, prediction of the binding free energy using Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) method showed that five hits, i.e., Lig25/ZINC253496376, Lig682/ZINC98047241, Lig449/ZINC85878047, Lig554/ZINC253389510, and Lig199/ZINC12638303, had lower binding energy compared to LASW1976. This result indicated their potentials as new inhibitors of PI3Kδ.
Keywords	pi3k ; molecular docking ; pharmacophore modeling ; molecular dynamics simulation ; Chemistry ; QD1-999
Subject code	540 ; 541
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Department of Chemistry, Universitas Gadjah Mada
Document type	Article ; Online
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Article: Unraveling the binding mechanism of the active form of Remdesivir to RdRp of SARS-CoV-2 and designing new potential analogues: Insights from molecular dynamics simulations.

Arba, Muhammad / Paradis, Nicholas / Wahyudi, Setyanto T / Brunt, Dylan J / Hausman, Katherine R / Lakernick, Phillip M / Singh, Mursalin / Wu, Chun

Chemical physics letters

2022 Volume 799, Page(s) 139638

Abstract: The binding of the active form of Remdesivir (RTP) to RNA-dependent RNA Polymerase (RdRp) of SARS-CoV-2 was studied using molecular dynamics simulation. The RTP maintained the interactions observed in the experimental cryo-EM structure. Next, we designed ...

Abstract	The binding of the active form of Remdesivir (RTP) to RNA-dependent RNA Polymerase (RdRp) of SARS-CoV-2 was studied using molecular dynamics simulation. The RTP maintained the interactions observed in the experimental cryo-EM structure. Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that of RTP, but also binds more strongly than RTP does as predicted by MM-PBSA binding energy. This suggest that these analogues might be able to covalently link to the primer strand as RTP, but their 3' modification would terminate the primer strand growth.
Language	English
Publishing date	2022-04-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1466293-0
ISSN	0009-2614
ISSN	0009-2614
DOI	10.1016/j.cplett.2022.139638
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Article ; Online: Novel inhibitors to ADP ribose phosphatase of SARS-CoV-2 identified by structure-based high throughput virtual screening and molecular dynamics simulations.

Patel, Dhrumi C / Hausman, Katherine R / Arba, Muhammad / Tran, Annie / Lakernick, Phillip M / Wu, Chun

Computers in biology and medicine

2021 Volume 140, Page(s) 105084

Abstract: The outbreak of a new coronavirus (SARS-CoV-2) was first identified in Wuhan, People's Republic of China, in 2019, which has led to a severe, life-threatening form of pneumonia (COVID-19). Research scientists all around the world have been trying to find ...

Abstract	The outbreak of a new coronavirus (SARS-CoV-2) was first identified in Wuhan, People's Republic of China, in 2019, which has led to a severe, life-threatening form of pneumonia (COVID-19). Research scientists all around the world have been trying to find small molecule drugs to treat COVID-19. In the present study, a conserved macrodomain, ADP Ribose phosphatase (ADRP), of a critical non-structural protein (Nsp3) in all coronaviruses was probed using large-scale Molecular Dynamics (MD) simulations to identify novel inhibitors. In our virtual screening workflow, the recently-solved X-ray complex structure, 6W6Y, with a substrate-mimics was used to screen 17 million ZINC15 compounds using drug property filters and Glide docking scores. The top twenty output compounds each underwent 200 ns MD simulations (i.e. 20 × 200 ns) to validate their individual stability as potential inhibitors. Eight out of the twenty compounds showed stable binding modes in the MD simulations, as well as favorable drug properties from our predctions. Therefore, our computational data suggest that the resulting top eight out of twenty compounds could potentially be novel inhibitors to ADRP of SARS-CoV-2.
Language	English
Publishing date	2021-11-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2021.105084
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