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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
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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
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: STUDI HUBUNGAN KUANTITATIF STRUKTUR AKTIVITAS SENYAWA TURUNAN MEISOINDIGO SEBAGAI INHIBITOR CDK4

Muhammad Arba / Riki Andriansyah / Messi Leonita

Jurnal Kimia Riset, Vol 1, Iss 2, Pp 129-

2016 Volume 134

Abstract: ABSTRAK Telah dilakukan analisis Hubungan Kuantitatif Struktur-Aktivitas (HKSA) senyawa turunan meisoindigo sebagai inhibitor Cyclin Dependent Kinase-4 (CDK4) menggunakan regresi multi linear untuk pemilihan variabel. Hasil penelitian menyatakan bahwa ... ...

Abstract	ABSTRAK Telah dilakukan analisis Hubungan Kuantitatif Struktur-Aktivitas (HKSA) senyawa turunan meisoindigo sebagai inhibitor Cyclin Dependent Kinase-4 (CDK4) menggunakan regresi multi linear untuk pemilihan variabel. Hasil penelitian menyatakan bahwa aktivitas penghambatan CDK4 dari senyawa turunan mesoindigo bergantung pada beberapa parameter, yaitu momen dipol, energi total, energi elektronik, panas pembentukan, dan kelarutan. Akurasi model HKSA yang diusulkan divalidasi baik dengan teknik validasi silang maupun dengan validasi eksternal. Hasil penelitian ini dapat digunakan untuk desain senyawa inhibitor CDK4 yang lebih baik dari turunan meisoindigo. Kata kunci: HKSA, meisoindigo, kanker, CDK4 ABSTRACT Cyclin-dependent kinase 4 (CDK4) is an important target in the treatment of cancer. Exploring of compounds that can inhibit the activity of CDK4 is actively performed worldwide. This research was conducted to do Quantitative Structure-Activity Relationship (QSAR) analysis of meisoindigo derivative compounds as inhibitor for CDK4 in order to get QSAR equation, then it was further used to design new inhibitor based meisoindigo which has more potent and selective for CDK4. Data compound is divided into training set to build QSAR models and the test set to validate the model. Calculation was done by MOE2009.10 descriptor and multilinear regression analysis, SPSS19.0. The results showed that the inhibitory activity of mesoindigo derived compounds toward CDK4 was depended on several dipole moment, total energy, electronic energy, heat of formation, and solubility. The accuracy of QSAR models proposed validated by cross validation techniques and with external validation. The results of this study can be used to design a new CDK4 inhibitor compound better than meisoindigo derivative Keywords: QSAR, meisoindigo, cancer, CDK4
Keywords	Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2016-12-01T00:00:00Z
Publisher	Universitas Airlangga
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Virtual Screening of the Indonesian Medicinal Plant and Zinc Databases for Potential Inhibitors of the RNA-Dependent RNA Polymerase (RdRp) of 2019 Novel Coronavirus

Muhammad Arba / Andry Nur-Hidayat / Ida Usman / Arry Yanuar / Setyanto Tri Wahyudi / Gilbert Fleischer / Dylan James Brunt / Chun Wu

Indonesian Journal of Chemistry, Vol 20, Iss 6, Pp 1430-

2020 Volume 1440

Abstract: The novel coronavirus disease 19 (Covid-19) which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic across the world, which necessitate the need for the antiviral drug discovery. One of the potential protein ... ...

Abstract	The novel coronavirus disease 19 (Covid-19) which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a pandemic across the world, which necessitate the need for the antiviral drug discovery. One of the potential protein targets for coronavirus treatment is RNA-dependent RNA polymerase. It is the key enzyme in the viral replication machinery, and it does not exist in human beings, therefore its targeting has been considered as a strategic approach. Here we describe the identification of potential hits from Indonesian Herbal and ZINC databases. The pharmacophore modeling was employed followed by molecular docking and dynamics simulation for 40 ns. 151 and 14480 hit molecules were retrieved from Indonesian herbal and ZINC databases, respectively. Three hits that were selected based on the structural analysis were stable during 40 ns, while binding energy prediction further implied that ZINC1529045114, ZINC169730811, and 9-Ribosyl-trans-zeatin had tighter binding affinities compared to Remdesivir. The ZINC169730811 had the strongest affinity toward RdRp compared to the other two hits including Remdesivir and its binding was corroborated by electrostatic, van der Waals, and nonpolar contribution for solvation energies. The present study offers three hits showing tighter binding to RdRp based on MM-PBSA binding energy prediction for further experimental verification.
Keywords	Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Department of Chemistry, Universitas Gadjah Mada
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular modeling on the identification of potential Janus Kinase 3 (JAK3) inhibitor based on the Indonesian Medicinal Plant Database

Muhammad Arba / Sanang Nur Safitri / Andry Nur Hidayat / Arry Yanuar / Muhammad Sulaiman Zubair / Asmiyenti Djaliasrin Djalil / Daryono Hadi Tjahjono

Journal of Mathematical and Fundamental Sciences, Vol 52, Iss

2020 Volume 3

Abstract: The Janus tyrosine kinases (JAKs) have shown great promise as therapeutic protein targets in the treatment of cancer and inflammation diseases. This study used pharmacophore modeling to identify potential inhibitors of Janus kinase 3 (JAK3). A ... ...

Abstract	The Janus tyrosine kinases (JAKs) have shown great promise as therapeutic protein targets in the treatment of cancer and inflammation diseases. This study used pharmacophore modeling to identify potential inhibitors of Janus kinase 3 (JAK3). A pharmacophore model was developed based on a known JAK3 inhibitor (1NX) and was employed to search for potential JAK3 inhibitors against Indonesian herbal compounds. Among 28 hit molecules that were identified and subjected to a molecular docking protocol against JAK3, the three compounds that had the highest affinities toward JAK3 were camelliaside B, 3-O-galloylepicatechin-(4beta-6)-epicatechin-3-O-gallate, and mesuaferrone B. These were then each subjected to a 50-ns molecular dynamics (MD) simulation. Analysis of RMSD and RMSF values indicated that the three compounds reached stability during the MD simulation. Interestingly, all three compounds had lower binding energies than 1NX against JAK3, as predicted by the MM-PBSA binding energy calculation.
Keywords	Janus kinase ; MM-PBSA ; molecular dynamics simulation ; pharmacophore modeling ; virtual screening ; Science ; Q ; Science (General) ; Q1-390
Subject code	540
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	ITB Journal Publisher
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Insight into the Interaction of Cationic Porphyrin-Anthraquinone Hybrids with Hsp90

Muhammad Arba / Ruslin / Rahmana Emran Kartasasmita / Slamet Ibrahim Surantaatmadja / Daryono Hadi Tjahjono

Journal of Mathematical and Fundamental Sciences, Vol 50, Iss 3, Pp 303-

In Silico Analysis

2018 Volume 314

Abstract: Heat shock protein 90 (Hsp90) is responsible for the correct folding of many cellular proteins. Several Hsp90 inhibitors have been developed for cancer treatment. The present in silico study aimed to evaluate the potential of several porphyrin ... ...

Abstract	Heat shock protein 90 (Hsp90) is responsible for the correct folding of many cellular proteins. Several Hsp90 inhibitors have been developed for cancer treatment. The present in silico study aimed to evaluate the potential of several porphyrin derivatives conjugated with anthraquinone groups as Hsp90 inhibitors by using simulation of molecular docking and molecular dynamics. The binding mode of porphyrin hybrids to Hsp90, which was examined by using AutoDock 4.2, showed that all six porphyrin compounds fit well in the binding pocket of Hsp90. The pi-cationic interactions with Lys58 were exclusively observed in the interaction of each porphyrin hybrid. Stabilities of porphyrin-Hsp90 complexes were confirmed by 40-ns MD simulation, which was carried out with the help of AMBER16. Prediction of ligand affinity by using the MM-PBSA method showed that all complexes were energetically favorable as indicated by a negative binding free energy. The predicted affinities of tris−H2PyP−AQ, tris−H2PzP−AQ, bis−H2PzP−AQ, and mono−H2PzP−AQ are better than those of geldanamycin, a known inhibitor of Hsp90, which shows the importance of the electrostatic and van der Waals energies for ligand binding.
Keywords	Hsp90 ; MM-PBSA ; molecular docking ; molecular dynamics simulation ; porphyrin ; Science ; Q ; Science (General) ; Q1-390
Subject code	540
Language	English
Publishing date	2018-12-01T00:00:00Z
Publisher	ITB Journal Publisher
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Hubungan Kuantitatif Struktur-Aktivitas (HKSA) dan Penambatan Molekul Senyawa Turunan Benzamida sebagai Inhibitor Alosterik Mitogen Enhanced Kinase (MEK)

Muhammad Arba / Ruslin Ruslin / Nursan Nursan / Maulidiyah Maulidiyah / Daryono Hadi Tjahjono

Jurnal Kimia Valensi, Vol 4, Iss 1, Pp 42-

2018 Volume 51

Abstract: Jalur sinyal protein kinase Ras-Raf-MEK-ERK adalah salah satu target penting dalam penemuan obat antikanker. Senyawa turunan benzamida diketahui berpotensi sebagai inhibitor alosterik Mitogen Enhanced Kinase (MEK). Pada penelitian ini dilakukan studi ... ...

Abstract	Jalur sinyal protein kinase Ras-Raf-MEK-ERK adalah salah satu target penting dalam penemuan obat antikanker. Senyawa turunan benzamida diketahui berpotensi sebagai inhibitor alosterik Mitogen Enhanced Kinase (MEK). Pada penelitian ini dilakukan studi hubungan kuantitatif stuktur dan aktivitas (HKSA) dan penambatan molekul pada 30 senyawa turunan benzamida sebagai inhibitor alosterik MEK untuk mendapatkan senyawa baru turunan benzamida yang lebih poten sebagai inhibitor alosterik MEK. Perhitungan 13 deskriptor molekul yang mewakili parameter sterik, hidrofobik dan elektronik dilakukan dengan perangkat lunak MOE 2009.10, sedangkan analisis regresi multi linear dengan SPSS 19.0 digunakan untuk mencari hubungan antara variabel bebas (deksriptor molekul) dengan variabel terikat (aktivitas penghambatan senyawa pada MEK). Model HKSA terbaik yang diperoleh adalah pIC50 = 14.229 – 0.00001(AM1_E) + 0.043(ASA_H) + 33.609(Glob) – 0.648(Log S) – 0.047(Vol) dengan kriteria statistik R=0.965; R2=0.931; Fhitung/ Ftabel= 17.693, dan q2 = 0.8897. Desain senyawa baru dilakukan menggunakan model HKSA tervalidasi dan diperoleh 2 senyawa baru turunan benzamida, C1, dan C2, yang memiliki aktivitas lebih baik dari senyawa induk. Studi penambatan molekul menunjukkan bahwa kedua senyawa baru tersebut mampu berinteraksi pada sisi alosterik protein MEK melalui ikatan hidrogen dan ikatan van der Waals dengan residu-residu asam amino krusial protein MEK. Penelitian ini mengindikasikan bahwa kedua senyawa baru yang didesain dapat ditindaklanjuti pada studi penemuan obat yang menargetkan MEK pada sisi alosterik. DOI:http://dx.doi.org/10.15408/jkv.v4i1.7454
Keywords	Chemistry ; QD1-999
Language	Indonesian
Publishing date	2018-05-01T00:00:00Z
Publisher	Syarif Hidayatullah Jakarta State Islamic University
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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