Tag Archives: molecular docking

Polyether ionophores as potential antimalarial

December 1, 2022Pharmaceutical Sciencearticle, malaria, molecular docking, PfGST, polyether ionophore, Streptomyces hygroscopicusjppres

J. Pharm. Pharmacogn. Res., vol. 10, no. 6, pp. 1139-1148, November-December 2022.

DOI: https://doi.org/10.56499/jppres22.1478_10.6.1139

Original Article

Potential of polyether ionophore compounds as antimalarials through inhibition on Plasmodium falciparum glutathione S-transferase by molecular docking studies

[Potencial de los compuestos ionóforos de poliéter como antimaláricos mediante la inhibición de glutatión S-transferasa de Plasmodium falciparum a través de estudios de acoplamiento molecular]

Alfian Wika Cahyono^1,2, Icha Farihah Deniyati Faratisha¹, Nabila Erina Erwan^1,3, Rivo Yudhinata Brian Nugraha^1,4, Ajeng Maharani Putri^1,3, Loeki Enggar Fitri^1,4*

¹Malaria Research Group, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia.

²Doctoral Program in Medical Science, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia.

³Master Program in Biomedical Science, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia.

⁴Department of Parasitology, Faculty of Medicine, Universitas Brawijaya, Malang, East Java, 65145, Indonesia.

*E-mail: lukief@ub.ac.id

Abstract

Context: Malaria is still a serious global health problem due to the development of drug resistance. It is necessary to find new drugs with renewable mechanisms that are effective in killing parasites. Our previous research has analyzed more than one compound of polyether ionophore group in ethyl acetate Streptomyces hygroscopicus subsp. hygroscopicus extract. Polyether ionophore is known to have a similar mechanism of action to chloroquine which is potent in inhibiting Plasmodium falciparum glutathione S-transferase (PfGST).

Aims: To evaluate the potential effect of polyether ionophore toward PfGST as a target protein through molecular docking.

Methods: PfGST was obtained from Protein Data Bank. Test ligands (polyether ionophore) and control ligands (chloroquine) were obtained from PubChem. Pharmacokinetic analysis was done using SwissADME, molecular docking using PyRx 0.9, visualization using LigPlot and PyMOL, and molecular dynamics using YASARA for the best ligand activity.

Results: Lenoremycin had the highest binding affinity to PfGST (-8.53 kcal/mol) among other polyether ionophores, and nigericin had the best residue bonding with hydrophobic and hydrogen with a binding affinity of -8.25 kcal/mol compared to chloroquine complex in molecular docking and molecular dynamic simulation.

Conclusions: Polyether ionophore could serve as an antimalarial agent better than chloroquine, with nigericin as the best compound candidate in inhibiting PfGST compared to other polyether ionophores.

Keywords: malaria; molecular docking; PfGST; polyether ionophore; Streptomyces hygroscopicus.

Resumen

Contexto: La malaria sigue siendo un grave problema sanitario mundial debido al desarrollo de resistencia a los fármacos. Es necesario encontrar nuevos fármacos con mecanismos renovables que sean eficaces para matar a los parásitos. Nuestra investigación anterior ha analizado más de un compuesto del grupo ionóforo poliéter en el extracto de acetato de etilo de Streptomyces hygroscopicus subsp. hygroscopicus. Se sabe que el poliéter ionóforo tiene un mecanismo de acción similar al de la cloroquina, que es potente inhibidor de la gutatión S-transferasa de Plasmodiun falciparum (PfGST).

Objetivos: Evaluar el efecto potencial del poliéter ionóforo hacia la PfGST como proteína diana a través del acoplamiento molecular.

Métodos: PfGST se obtuvo del Banco de Datos de Proteínas. Los ligandos de prueba (poliéter ionóforo) y los ligandos de control (cloroquina) se obtuvieron de PubChem. El análisis farmacocinético se realizó con SwissADME, el docking molecular con PyRx 0.9, la visualización con LigPlot y PyMOL, y la dinámica molecular con YASARA para la mejor actividad del ligando.

Resultados: La lenoremycina tuvo la mayor afinidad de unión a PfGST (-8,53 kcal/mol) entre otros poliéteres ionóforos, y la nigericina tuvo la mejor unión de residuos con hidrófobos e hidrógenos con una afinidad de unión de -8,25 kcal/mol en comparación con el complejo de cloroquina en el docking molecular y la simulación dinámica molecular.

Conclusiones: El ionóforo poliéter podría servir como agente antimalárico mejor que la cloroquina, siendo la nigericina el mejor candidato para inhibir el PfGST en comparación con otros ionóforos poliéter.

Palabras Clave: acoplamiento molecular; ionóforo poliéter; malaria; PfGST; Streptomyces hygroscopicus.

Citation Format: Cahyono AW, Faratisha IFD, Erwan NE, Nugraha RYB, Putri AM, Fitri LE (2022) Potential of polyether ionophore compounds as antimalarials through inhibition on Plasmodium falciparum glutathione S-transferase by molecular docking studies. J Pharm Pharmacogn Res 10(6): 1139–1148. https://doi.org/10.56499/jppres22.1478_10.6.1139

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Sonchus arvensis L. against SARS-CoV-2 infection

November 29, 2022Pharmaceutical Scienceantiviral, article, bioinformatics, COVID-19, molecular docking, SARS-CoV-2, Sonchus arvensis L.jppres

J. Pharm. Pharmacogn. Res., vol. 10, no. 6, pp. 1126-1138, November-December 2022.

DOI: https://doi.org/10.56499/jppres22.1489_10.6.1126

Original Article

Molecular simulation of compounds from n-hexane fraction of Sonchus arvensis L. leaves as SARS-CoV-2 antiviral through inhibitor activity targeting strategic viral protein

[Simulación molecular de compuestos de la fracción de n-hexano de las hojas de Sonchus arvensis L. como antivirales del SARS-CoV-2 a través de la actividad inhibidora dirigida a la proteína viral estratégica]

Dwi Kusuma Wahyuni^1,2, Sumrit Wacharasindhu³, Wichanee Bankeeree², Hunsa Punnapayak², Hery Purnobasuki¹, Junairiah¹, Arif NM Ansori⁴, Viol Dhea Kharisma^1,5, Arli Aditya Parikesit⁶, Listyani Suhargo¹, Sehanat Prasongsuk^1,2*

¹Department of Biology, Faculty of Science and Technology, Universitas Airlangga Surabaya, East Java, 60115, Indonesia.

²Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.

³Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok,10330, Thailand.

⁴Professor Nidom Foundation, Surabaya, East Java, 60115, Indonesia.

⁵Computational Virology Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia Foundation, Gresik, East Java, 61171, Indonesia.

⁶Department of Bioinformatics, School of Life Science, Indonesia International Institute for Life Sciences, Jakarta, 13210, Indonesia.

*E-mail: dwi-k-w@fst.unair.ac.id (DKW), listyani-s@fst.unair.ac.id (LS), sehanat.p@chula.ac.th (SP)

Abstract

Context: COVID-19 was caused by the spread and transmission of SARS-CoV-2 at the end of 2019 until now. The problem comes when antiviral drugs have not yet been found and patients infected with SARS-CoV-2 can trigger a cytokine storm condition due to the effects of viral replication. Indonesia has various kinds of medicinal plants, such as Sonchus arvensis L., which are used as medicinal plants.

Aims: To analyze the activity of the inhibitor as SARS-CoV-2 antiviral agents from n-hexane fractions of S. arvensis leaves.

Methods: The sample was collected from GC-MS analysis, PubChem, and Protein Databank database, then drug-likeness identification using Lipinski Rule of Five server and bioactive prediction of bioactive compounds as inhibitor activity was conducted by Molinspiration server. Furthermore, the docking simulation was performed using PyRx 0.9.9 software to determine the binding activity, molecular interaction by Discovery Studio software to identify position and interaction type, 3D molecular visualization by PyMol 2.5. software, and dynamic by CABS-flex 2.0 server to predict interaction stability.

Results: α-Amyrin and β-amyrin from n-hexane fractions of S. arvensis leaves had activity as SARS-CoV-2 inhibitors through interactions on helicase, RdRp, Mpro, and RBD-Spike, both compounds had more negative binding affinity than control drug and can produce stable chemical bond interactions in the ligand-protein complexes. However, the results were merely computational, so they must be validated through an in vivo and in vitro research approach.

Conclusions: Sonchus arvensis L. leaves were predicted to have SARS-CoV-2 antiviral through inhibitor activity by α-amyrin and β-amyrin.

Keywords: antiviral; bioinformatics; SARS-CoV-2; Sonchus arvensis L.

Resumen

Contexto: La propagación y la transmisión del SARS-CoV-2 han sido causadas por el COVID-19 desde finales de 2019 hasta ahora. El problema surge cuando aún no se han encontrado medicamentos antivirales y los pacientes infectados por el SARS-CoV-2 pueden desencadenar una condición de tormenta de citocinas debido a los efectos de la replicación viral. Indonesia tiene varios tipos de plantas medicinales, como Sonchus arvensis L., que se utilizan como plantas medicinales.

Objetivos: Analizar la actividad inhibidora de SARS-CoV-2 de fracciones de n-hexano de las hojas de S. arvensis.

Métodos: La muestra se recogió del análisis GC-MS, PubChem y la base de datos Protein Databank, luego se identificó la similitud de los fármacos utilizando el servidor Lipinski Rule of Five y se realizó la predicción de los compuestos bioactivos como actividad inhibidora mediante el servidor Molinspiration. Además, se realizó la simulación de acoplamiento mediante el software PyRx 0.9.9 para determinar la actividad de unión, la interacción molecular mediante el software Discovery Studio para identificar la posición y el tipo de interacción, la visualización molecular 3D mediante el software PyMol 2.5. y la dinámica mediante el servidor CABS-flex 2.0 para predecir la estabilidad de la interacción.

Resultados: La α-amirina y la β-amirina de las fracciones de n-hexano de las hojas de S. arvensis tuvieron actividad como inhibidores del SARS-CoV-2 a través de las interacciones en la helicasa, RdRp, Mpro y RBD-Spike, ambos compuestos tuvieron más afinidad de unión negativa que el fármaco de control y pueden producir interacciones de enlace químico estables en los complejos ligando-proteína. Sin embargo, los resultados fueron meramente computacionales, por lo que deben ser validados mediante un enfoque de investigación in vivo e in vitro.

Conclusiones: Se predijo que las hojas de S. arvensis tienen actividad antiviral contra el SARS-CoV-2 a través de la actividad inhibidora de la α-amirina y la β-amirina.

Palabras Clave: antiviral; bioinformática; SARS-CoV-2; Sonchus arvensis L.

Citation Format: Wahyuni DK, Wacharasindhu S, Bankeeree W, Punnapayak H, Parikesit AA, Kharisma VD, Ansori ANM, Suhargo L, Prasongsuk S (2022) Molecular simulation of compounds from n-hexane fraction of Sonchus arvensis L. leaves as SARS-CoV-2 antiviral through inhibitor activity targeting strategic viral protein. J Pharm Pharmacogn Res 10(6): 1126–1138. https://doi.org/10.56499/jppres22.1489_10.6.1126

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In silico anti-dengue Sterculia quadrifida stem bark compounds

October 12, 2022Pharmaceutical Sciencearticle, dengue, envelope protein, faloak, molecular docking, NS5 RdRp, Sterculia quadrifidajppres

J. Pharm. Pharmacogn. Res., vol. 10, no. 6, pp. 1006-1014, November-December 2022.

DOI: https://doi.org/10.56499/jppres22.1445_10.6.1006

Original Article

In silico analysis of anti-dengue activity of faloak (Sterculia quadrifida R. Br) stem bark compounds

[Análisis in silico de la actividad anti-dengue de compuestos de corteza de tallo de faloak (Sterculia quadrifida R. Br.)]

Audrey G. Riwu¹, Jusak Nugraha², Djoko A. Purwanto^3*, Erwin A. Triyono⁴

¹Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen Prof. Dr. Moestopo 47, 60131, Surabaya, Indonesia.

²Department of Clinical Pathology, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen Prof. Dr. Moestopo 47, 60131, Surabaya, Indonesia.

³Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Jl. Mulyorejo, 60115, Surabaya, Indonesia.

⁴Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen Prof. Dr Moestopo 47, 60131, Surabaya, Indonesia.

*E-mail: djokoagus@ff.unair.ac.id

Abstract

Context: Dengue is one of the most common infectious diseases found in tropical and subtropical regions, particularly in urban and semi-urban areas. Management dengue until now has not had a specific therapy. The development of dengue therapy using traditional plants as the main source of dengue therapy is needed. Sterculia quadrifida R. Br stem bark is one of the traditional plants in Indonesia, widely used by local people to treat various diseases.

Aims: To identify the potency of S. quadrifida stem bark extract against the envelope protein and NS5 RdRp (RNA-dependent RNA polymerase) in dengue infection through in silico approach.

Methods: All ligands from S. quadrifida stem bark extract from the previous study and protein preparations were retrieved from the PubChem and RSCB data bank database, respectively. Drug-likeness using Lipinski’s rule of five methods. Pyrx, PyMOL, and Discovery Studio 2.0 were used to analyze and visualize the potency of S. quadrifida stem bark-specific compounds against the envelope and NS5 RdRp.

Results: Epicatechin and scopoletin have the lowest affinity bond, some noncovalent interaction, and also similarity in the position of the amino acid interaction to the reference control ribavirin.

Conclusions: Epicatechin and scopoletin from S. quadrifida have antiviral potential against dengue by disposing of envelope protein and NS5 RdRp.

Keywords: dengue; envelope protein; faloak; molecular docking; NS5 RdRp; Sterculia quadrifida.

Resumen

Contexto: El dengue es una de las enfermedades infecciosas más comunes que se encuentran en las regiones tropicales y subtropicales, particularmente en áreas urbanas y semiurbanas. El manejo del dengue hasta el momento no ha tenido una terapia específica. Se necesita el desarrollo de la terapia contra el dengue utilizando plantas tradicionales como fuente principal para la terapia contra el dengue. La corteza del tallo Sterculia quadrifida R. Br. es una de las plantas tradicionales en Indonesia, ampliamente utilizada por la población local para tratar diversas enfermedades.

Objetivos: Identificar la potencia del extracto de corteza de tallo de S. quadrifida contra la proteína de la envoltura y NS5 RdRp (ARN polimerasa dependiente de ARN) en la infección por dengue mediante un enfoque in silico.

Métodos: Todos los ligandos del extracto de corteza de tallo de S. quadrifida del estudio anterior y las preparaciones de proteínas se recuperaron de la base de datos del banco de datos PubChem y RSCB, respectivamente. Semejanza a los fármacos utilizando la regla de los cinco métodos de Lipinski. Pyrx, PyMOL y Discovery Studio 2.0 se utilizaron para analizar y visualizar la potencia de los compuestos específicos de la corteza del tallo de S. quadrifida contra la envoltura y NS5 RdRp.

Resultados: La epicatequina y la escopoletina tienen el enlace de afinidad más bajo, alguna interacción no covalente y también similitud en la posición de la interacción de aminoácidos con la ribavirina como control de referencia.

Conclusiones: La epicatequina y la escopoletina de S. quadrifida tienen potencial antiviral contra el dengue al eliminar la proteína de la envoltura y la NS5 RdRp.

Palabras Clave: acoplamiento molecular; dengue; faloak; NS5RdRp; proteína de envoltura; Sterculia quadrifida.

Citation Format: Riwu AG, Nugraha J, Purwanto DA, Triyono EA (2022) In silico analysis of anti-dengue activity of faloak (Sterculia quadrifida R. Br) stem bark compounds. J Pharm Pharmacogn Res 10(6): 1006–1014. https://doi.org/10.56499/jppres22.1445_10.6.1006

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Syzygium polyanthum bioactive compounds in polycystic ovary syndrome

June 29, 2022Pharmaceutical Scienceantioxidant, article, inflammation, molecular docking, polycystic ovary syndrome, Syzygium polyanthumjppres

J. Pharm. Pharmacogn. Res., vol. 10, no. 4, pp. 725-736, July-August 2022.

DOI: https://doi.org/10.56499/jppres22.1408_10.4.725

Original Article

Anti-inflammatory and antioxidant potential of Syzygium polyanthum (Wight) Walp. bioactive compounds in polycystic ovary syndrome: An in silico study

[Potencial anti-inflamatorio y antioxidante de compuestos bioactivos de Syzygium polyanthum (Wight) Walp. en el síndrome de ovario poliquístico: Un estudio in silico]

Renny Aditya^1,4, Budi Santoso²*, Widjiati Widjiati³

¹Doctoral Program of Medical Science, Faculty of Medicine, University of Airlangga, Surabaya, Indonesia.

²Department of Obstetrics and Gynecology, Faculty of Medicine, University of Airlangga, Surabaya, Indonesia.

³Department of Veterinary Anatomy, Faculty of Veterinary Medicine, University of Airlangga, Surabaya, Indonesia.

⁴Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Lambung Mangkurat, Banjarmasin, Indonesia.

*E-mail: budi.santoso@fk.unair.ac.id

Abstract

Context: Polycystic ovary syndrome (PCOS) is significantly associated with inflammation and oxidative stress. Syzygium polyanthum is a plant rich in pharmacological properties. Aims: To evaluate the anti-inflammation and antioxidant potential of S. polyanthum bioactive compounds using in silico approach.

Methods: The S. polyanthum was extracted using the ultrasound-assisted extraction (UAE) method, and the bioactive compounds were screened using Liquid Chromatography–High Resolution Mass Spectrometry (LC-HRMS) analysis. This study predicted the biological activity of S. polyanthum compounds using PASS Online server. Before docking, we analyzed the protein-protein interactions (PPIs) network of TNFα, NF-kB, SOD, and KEAP1. The molecular docking was done using Autodock Vina in PyRx software and visualized using Discovery Studio. Probability to be active (Pa) was determined.

Results: The bioactive compounds found in S. polyanthum and used in this study were deoxyphomalone, NCGC00169066-01, and phloretin with retention times [min] of 0.886, 0.907, and 8.323, respectively. The predicted biological activity of compounds and controls were anti-inflammatory, immunosuppressant, TNF expression inhibitor, immunomodulatory and HIF1α expression inhibitor (Pa>0.5 for all S. polyanthum compounds and Pa<0.5 for SPD304, MG-132, and MDF). Based on PPIs network analysis, TNFα, NF-kB, SOD, and KEAP1 are associated. The molecular docking analysis showed that deoxyphomalone, NCGC00169066-01, and phloretin had inhibition potential against TNFα and NF-kB, and activation potential against SOD, due to several residues involved in the interaction of compounds-protein was the same as the interaction of inhibitor (SPD-304 and MG-132) and activator (gallic acid) control against the protein. The residues may have the same inhibition or activation mechanism as the control. However, S. polyanthum bioactive compounds may still have inhibition potential against KEAP1 through Ala548 residue that is also involved in the interaction of DMF-KEAP1.

Conclusions: The bioactive compounds of S. polyanthum showed anti-inflammation and antioxidant potential, which may have a good effect in the treatment of PCOS, yet still need to be confirmed in vitro or in vivo research.

Keywords: antioxidant; inflammation; molecular docking; polycystic ovary syndrome; Syzygium polyanthum.

Resumen

Contexto: El síndrome de ovario poliquístico (SOP) está significativamente asociado con la inflamación y el estrés oxidativo. Syzygium polyanthum es una planta rica en propiedades farmacológicas. Objetivos: Evaluar el potencial anti-inflamatorio y antioxidante de los compuestos bioactivos de S. polyanthum utilizando un enfoque in silico.

Métodos: S. polyanthum se extrajo mediante el método de extracción asistida por ultrasonido (UAE), y los compuestos bioactivos se seleccionaron mediante análisis de cromatografía líquida-espectrometría de masas de alta resolución (LC-HRMS). Este estudio predijo la actividad biológica de los compuestos de S. polyanthum utilizando el servidor PASS Online. Antes del acoplamiento, analizamos la red de interacciones proteína-proteína (PPI) de TNFα, NF-kB, SOD y KEAP1. El acoplamiento molecular se realizó con Autodock Vina en el software PyRx y se visualizó con Discovery Studio. Se determinó la probabilidad de estar activo (Pa).

Resultados: Los compuestos bioactivos encontrados en S. polyanthum y utilizados en este estudio fueron desoxifomalona, NCGC00169066-01 y floretina con tiempos de retención [min] de 0,886; 0,907 y 8,323, respectivamente. La actividad biológica predicha de los compuestos y controles fue anti-inflamatoria, inmunosupresora, inhibidora de la expresión de TNF, inmunomoduladora e inhibidora de la expresión de HIF1α (Pa>0,5 para todos los compuestos de S. polyanthum y Pa<0,5 para SPD304, MG-132 y MDF). Según el análisis de red de PPI, se asocian TNFα, NF-kB, SOD y KEAP1. El análisis de acoplamiento molecular mostró que la desoxifomalona, NCGC00169066-01 y la floretina tenían potencial de inhibición contra TNFα y NF-kB, y potencial de activación contra SOD, debido a que varios residuos involucrados en la interacción de compuestos-proteína eran los mismos que la interacción del inhibidor (SPD-304 y MG-132) y activador (ácido gálico) controlan contra la proteína. Los residuos pueden tener el mismo mecanismo de inhibición o activación que el control. Sin embargo, los compuestos bioactivos de S. polyanthum aún pueden tener un potencial de inhibición contra KEAP1 a través del residuo Ala548 que también está involucrado en la interacción de DMF-KEAP1.

Conclusiones: Los compuestos bioactivos de S. polyanthum mostraron potencial anti-inflamatorio y antioxidante, lo que puede tener un buen efecto en el tratamiento del SOP, pero aún debe confirmarse en investigaciones in vitro o in vivo.

Palabras Clave: acoplamiento molecular; antioxidante; inflamación; síndrome de ovario poliquistico; Syzygium polyanthum.

Citation Format: Aditya R; Santoso B; Widjiati W (2022) Anti-inflammatory and antioxidant potential of Syzygium polyanthum (Wight) Walp. bioactive compounds in polycystic ovary syndrome: An in silico study. J Pharm Pharmacogn Res 10(4): 725–736. https://doi.org/10.56499/jppres22.1408_10.4.725

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Virtual screening of lead flavonoids against DENV2

May 16, 2022Pharmaceutical Sciencearticle, DENV-2, envelope protein, flavonoids, molecular docking, virtual screeningjppres

J. Pharm. Pharmacogn. Res., vol. 10, no. 4, pp. 660-675, July-August 2022.

DOI: https://doi.org/10.56499/jppres22.1375_10.4.660

Original Article

Flavonoids as potential inhibitors of dengue virus 2 (DENV2) envelope protein

[Flavonoides como posibles inhibidores de la proteína de la cubierta del virus del dengue 2 (DENV2)]

Rachel Raditya Renantha¹, Alvin Richardo Liga¹, Christy Bianca Tanugroho¹, Lovine Xaviera Denovian¹, Siti Lateefa Az Zahra Budiyanto², Arli Aditya Parikesit^2*

¹Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav.88 Jakarta 13210 Indonesia.

²Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav.88 Jakarta 13210 Indonesia.

*E-mail: arli.parikesit@i3l.ac.id

Abstract

Context: Dengue viruses (DENVs) are the cause of dengue disease, which is one of the most frequent diseases caused by mosquito-borne viral infections. Currently, no specific treatment is available for dengue.

Aims: To identify the most promising inhibitors of dengue virus 2 (DENV2) envelope protein of DENV2 envelope protein from flavonoids compounds through computational methods.

Methods: Structures of 54 flavonoids were collected, then the compounds were screened based on Lipinski’s rules, and there were only 34 compounds that passed the screening. Then QSAR analysis was performed, followed by molecular docking analysis, ADMET evaluation, and molecular dynamics simulations to assess the stability of the protein.

Results: Based on the QSAR analysis, only 32 compounds were subjected to molecular docking analysis. Silymarin had the highest docking score, while juglanin had the lowest ACE score compared to positive controls. The ADMET evaluation showed silymarin and juglanin had good absorption and could not penetrate the blood-brain barrier. In contrast to silymarin which had negative results for the Ames test, carcinogenicity, skin sensitization, and eye irritation, juglanin was positive for Ames test and skin sensitization. Even though the molecular dynamic simulation of both ligands with DENV2 envelope protein showed unstable confirmation, it did not necessarily mean that the ligands cannot be used as inhibitors since the molecular docking results provide evidence of the ligands binding to the DENV2 envelope protein.

Conclusions: Based on the favorable results of QSAR analysis, molecular docking, and ADMET evaluation, juglanin and silymarin were chosen as the candidate with the most potential for DENV2 envelope protein inhibitors. However, further analyses such as in vitro and in vivo analyses are necessary to validate the result of this study.

Keywords: DENV-2; envelope protein; flavonoids; molecular docking; virtual screening.

Resumen

Contexto: Los virus del dengue (DENV) son los causantes de la enfermedad del dengue, que es una de las enfermedades más frecuentes causada por infecciones virales transmitidas por mosquitos. Actualmente, no se dispone de un tratamiento específico para el dengue.

Objetivos: Identificar los inhibidores más prometedores de la proteína de la envoltura del virus del dengue 2 (DENV2) de la proteína de la envoltura del DENV2 a partir de compuestos de flavonoides a través de métodos computacionales.

Métodos: Las estructuras de 54 flavonoides fueron recolectadas. Los compuestos se seleccionaron según las reglas de Lipinski y solo 34 compuestos pasaron la selección. Luego se realizó el análisis QSAR, seguido de análisis de acoplamiento molecular, evaluación ADMET y simulaciones de dinámica molecular para evaluar la estabilidad de la proteína.

Resultados: Según el análisis QSAR, solo 32 compuestos se sometieron a análisis de acoplamiento molecular. La silimarina obtuvo la puntuación de acoplamiento más alta, mientras que juglanina obtuvo la puntuación ACE más baja en comparación con los controles positivos. La evaluación ADMET mostró que la silimarina y la juglanina tenían una buena absorción y no podían penetrar la barrera hematoencefálica. En contraste con la silimarina que tuvo resultados negativos para la prueba de Ames, carcinogenicidad, sensibilización de la piel e irritación de los ojos, la juglanina fue positiva para la prueba de Ames y la sensibilización de la piel. Aunque la simulación de la dinámica molecular de ambos ligandos con la proteína de la cubierta de DENV2 mostró una confirmación inestable, no significa necesariamente que los ligandos no puedan usarse como inhibidores, ya que los resultados del acoplamiento molecular proporcionan evidencia de que los ligandos se unen a la proteína de la cubierta de DENV2.

Conclusiones: En base a los resultados favorables del análisis QSAR, el acoplamiento molecular y la evaluación ADMET, la juglanina y la silimarina fueron elegidas como las candidatas con mayor potencial para los inhibidores de la proteína de la envoltura de DENV2. Sin embargo, se necesitan más análisis, como análisis in vitro e in vivo, para validar el resultado de este estudio.

Palabras Clave: acoplamiento molecular; DENV-2; flavonoides; proteína de envoltura; proyección virtual.

Citation Format: Renantha RR, Liga AR, Tanugroho CB, Denovian LX, Budiyanto SLAZ, Parikesit AA (2022) Flavonoids as potential inhibitors of dengue virus 2 (DENV2) envelope protein. J Pharm Pharmacogn Res 10(4): 660–675. https://doi.org/10.56499/jppres22.1375_10.4.660

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In-silico study of volatile compounds and COVID-19

March 3, 2022Pharmaceutical ScienceDysphania ambrosioides, GC-MS/MS, molecular docking, Phyla scaberrima, SARS-CoV-2jppres

J. Pharm. Pharmacogn. Res., vol. 10, no. 3, pp. 469-485, May-June 2022.

DOI: https://doi.org/10.56499/jppres21.1328_10.3.469

Original Article

Volatile compounds from Phyla scaberrima (Juss. ex Pers.) Moldenke and Dysphania ambrosioides (L.) Mosyakin & Clemants as possible SARS-CoV-2 protease inhibitors: Identification and in-silico study

[Compuestos volátiles de Phyla scaberrima (Juss. ex Pers.) Moldenke y Dysphania ambrosioides (L.) Mosyakin & Clemants como posibles inhibidores de proteasas de SARS-CoV-2: Identificación y estudio in-silico]

Neyder Contreras-Puentes^1*, Manuel Salas-Moreno^2,3, Lina Mosquera-Chaverra², Leonomir Córdoba-Tovar⁴, Antistio Alviz-Amador⁵

¹GINUMED, Medicine, Corporation University Rafael Nuñez, Cartagena D.T y C, Colombia.

²Faculty of Naturals Sciences, Biology Department, Biosistematic Research Group, Technological University of Chocó, Quibdó, Colombia.

³Analytical Chemistry and Biomedicine Group. Exacts and Natural Sciences Faculty. University of Cartagena. Cartagena, Colombia.

⁴Research Group Natural Resources and Environmental Toxicology, Technological University of Chocó, Quibdó, Colombia.

⁵Pharmacology and Therapeutics Group, University of Cartagena, Cartagena D.T y C., Colombia.

*E-mail: neyder.contreras@curnvirtual.edu.co

Abstract

Context: COVID-19 is a pandemic that has affected the entire population, characterized by multisystemic involvement. With around 130 million cases of infection and more than 2.5 million deaths globally. However, the development of a low-efficacy treatment has led to the study of natural products as possible therapeutic alternatives against SARS-CoV-2.

Aims: To identify volatile compounds present in two plants in the Colombian Pacific and carry out in-silico studies to search for promising inhibitory molecules against SARS-CoV-2 proteases.

Methods: This research carried out the identification of metabolites of two plants identified in the Colombian Pacific, called P. scaberrima (Juss. ex Pers.) Moldenke y D. ambrosioides (L.) Mosyakin & Clemants. Ethanolic extracts were obtained by rotary-evaporation and determinated by GC-MS. Subsequently, in-silico studies were carried out by molecular docking against Mpro and PLpro using Autodock-vina 1.1. Also, a prediction of ADMET properties using SwissADME and GUSAR-Online server was performed.

Results: Thus, 15 volatile compounds with similarities greater than 85% were identified from both extracts, mostly sesquiterpenic and monoterpenic compounds. The compounds that showed the highest affinity against Mpro were α-amorphene and phytol for PLpro. Likewise, these were contrasted with co-crystallized molecules such as boceprevir and VIR2-251 as control structures. Finally, the predictions of ADMET properties showed values consistent with the literature.

Conclusions: Therefore, the follow-up of in-silico studies with these plants from Colombian pacific are considered as possible tools in the search for active molecules against proteases linked to virus.

Keywords: Dysphania ambrosioides; GC-MS/MS; molecular docking; Phyla scaberrima; SARS-CoV-2.

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Resumen

Contexto: COVID-19 es una pandemia que ha afectado a toda la población mundial, caracterizada por compromisos multisistémicos. Con alrededor de 130 millones de casos de infección y más de 2,5 millones de muertes en todo el mundo. Sin embargo, el desarrollo de un tratamiento de baja eficacia ha llevado al estudio de productos naturales como posibles alternativas terapéuticas frente al SARS-CoV-2.

Objetivos: Identificar compuestos volátiles presentes en dos plantas del Pacifico colombiano y realizar estudios in-silico para la búsqueda de promisorias moléculas inhibidoras contra proteasas de SARS-CoV-2.

Métodos: En esta investigación se realizó la identificación de metabolitos de dos plantas identificadas en el Pacífico colombiano, llamadas P. scaberrima (Juss. ex Pers.) Moldenke y D. ambrosioides (L.) Mosyakin & ClemantsSe obtuvieron extractos etanólicos, preconcentrados con evaporación rotatoria y se determinaron por GC-MS. Posteriormente, se realizaron estudios in-silico mediante acoplamiento molecular contra Mpro y PLpro utilizando Autodock-vina. Además, prediciendo las propiedades de ADMET mediante SwissADME y GUSAR-Online.

Resultados: Se identificaron 15 compuestos volátiles con similitudes superiores al 85% de ambos extractos, en su mayoría compuestos sesquiterpénicos y monoterpénicos. Los compuestos que mostraron la mayor afinidad contra Mpro fue α-amorfeno y fitol para PLpro. Asimismo, se contrastaron con moléculas co-cristalizadas como boceprevir y VIR2-251 como estructuras control. Finalmente, en las predicciones de propiedades ADMET mostraron valores consistentes con la literatura.

Conclusiones: Se consideró el seguimiento de estudios in-silico con estas plantas del Pacífico colombiano como posibles herramientas en la búsqueda de moléculas activas frente a proteasas ligadas al virus.

Palabras Clave: acoplamiento molecular; Dysphania ambrosioides; GC-MS/MS; Phyla scaberrima; SARS-CoV-2.

Citation Format: Contreras-Puentes N, Salas-Moreno MH, Mosquera-Chaverra L, Córdoba-Tovar L, Alvíz-Amador AA (2022) Volatile compounds from Phyla scaberrima (Juss. ex Pers.) Moldenke y Dysphania ambrosioides (L.) Mosyakin & Clemants as possible SARS-CoV-2 protease inhibitors: Identification and in-silico study. J Pharm Pharmacogn Res 10(3): 469–485. https://doi.org/10.56499/jppres21.1328_10.3.469

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Roselle flower for immunomodulatory adjuvant therapy in COVID-19

February 6, 2022Pharmaceutical ScienceCOVID-19, dentistry, Hibiscus sabdariffa, infectious disease, medicine, molecular docking, SARS-CoV-2jppres

J. Pharm. Pharmacogn. Res., vol. 10, no. 3, pp. 418-428, May-June 2022

DOI: https://doi.org/10.56499/jppres21.1316_10.3.418

Original Article

Anthocyanin, tartaric acid, ascorbic acid of roselle flower (Hibiscus sabdariffa L.) for immunomodulatory adjuvant therapy in oral manifestation coronavirus disease-19: An immunoinformatic approach

[Antocianina, ácido tartárico, ácido ascórbico de flor de Jamaica (Hibiscus sabdariffa L.) para la terapia adyuvante inmunomoduladora en la manifestación oral de la enfermedad por coronavirus-19: Un enfoque inmunoinformático]

Nastiti Faradilla Ramadhani¹, Alexander Patera Nugraha^1,2*, Desintya Rahmadhani³, Martining Shoffa Puspitaningrum³, Yuniar Rizqianti³, Viol Dhea Kharisma⁴, Tengku Natasha Eleena binti Tengku Ahmad Noor⁵, Rini Devijanti Ridwan⁶, Diah Savitri Ernawati⁷, Albertus Putera Nugraha⁸

¹Graduate Student of Dental Health Science, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

²Department of Orthodontic, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

³Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

⁴Graduate Student of Biology Science, Department of Biology, Faculty of Mathematics and Natural Science, Universitas Brawijaya, Malang, Indonesia

⁵Military Dental Officer of Royal Medical and Dental Corps, Malaysian Armed Forces, Indonesia.

⁶Department of Oral Biology, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

⁷Department of Oral Medicine, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, Indonesia.

⁸Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.

^*E-mail: alexander.patera.nugraha@fkg.unair.ac.id

Abstract

Context: Oral manifestations that arose from COVID-19 infection often causes morbidity and systemic drug administration is less effective. Roselle flower (Hibiscus sabdariffa) is one of the plants that is often used in infusion as it gives health benefits. Hence, H. sabdariffa may benefit from adjuvant therapy to treat oral manifestation due to COVID-19.

Aims: To investigate the potential of H. sabdariffa anthocyanins, tartaric acid, and ascorbic acid chemical compounds as antiviral, anti-inflammatory, antioxidant, and increasing tissue regeneration in oral manifestation due to COVID-19 infection in silico.

Methods: Chemical compounds consisted of anthocyanins, (+)-tartaric acid, and ascorbic acid beside target proteins consisted of ACE2-spike, Foxp3, IL-10, IL6, IL1β, VEGF, FGF-2, HSP70, TNFR and MDA-ovalbumin were obtained from the database, ligand samples were selected through absorption, distribution, metabolism, excretion and toxicology analysis, then molecular docking simulations, identification of protein-ligand interactions, and 3D visualization were performed.

Results: Anthocyanins, tartaric acid, and ascorbic acid are the active compounds in H. sabdariffa, which act as antioxidants. The activity of anthocyanin compounds is higher than other compounds through value binding affinity, which is more negative and binds to specific domains of target proteins by forming weak binding interactions that play a role in biological responses. Anthocyanins have the most negative binding energy compared to tartaric-acid and ascorbic acid.

Conclusions: Anthocyanins act as antioxidants; this mechanism increases heat shock protein-70 (HSP70), which may play an important role in increasing wound regeneration of oral manifestation in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as documented in silico.

Keywords: COVID-19; dentistry; Hibiscus sabdariffa; infectious disease; medicine.

Resumen

Contexto: Las manifestaciones orales derivadas de la infección por COVID-19 suelen causar morbilidad y la administración sistémica de fármacos es menos efectiva. La flor de Jamaica (Hibiscus sabdariffa) es una de las plantas que se suele utilizar en infusión ya que aporta beneficios para la salud. Por lo tanto, H. sabdariffa puede beneficiarse de la terapia adyuvante para tratar las manifestaciones orales debido a COVID-19.

Objetivos: Investigar el potencial de los compuestos químicos de H. sabdariffa, como antocianinas, ácido tartárico y ácido ascórbico como antivirales, antiinflamatorios, antioxidantes y el aumento de la regeneración de tejidos en la manifestación oral debido a la infección por COVID-19 a través de un enfoque inmunoinformático, un estudio in silico.

Métodos: Antocianinas, ácido tartárico y ácido ascórbico, además de proteínas diana como ACE2-spike, Foxp3, IL-10, IL6, IL1β, VEGF, FGF-2, HSP70, TNFR y MDA-ovoalbúmina, se obtuvieron de la base de datos, las muestras de ligando se seleccionaron mediante análisis de absorción, distribución, metabolismo, excreción y toxicología, luego se realizaron simulaciones de acoplamiento molecular, identificación de interacciones proteína-ligando y visualización 3D.

Resultados: Las antocianinas, el ácido tartárico y el ácido ascórbico son los compuestos activos de H. sabdariffa que actúan como antioxidantes. La actividad de los compuestos de antocianina es mayor que la de otros compuestos a través de una afinidad de unión de valor que es más negativa y se une a dominios específicos de proteínas diana formando interacciones de unión débiles que desempeñan un papel en las respuestas biológicas. Las antocianinas tienen la energía de unión más negativa en comparación con el ácido tartárico y el ácido ascórbico.

Conclusiones: Las antocianinas actúan como antioxidantes; este mecanismo aumenta la proteína de choque térmico-70 (HSP70), que puede desempeñar un papel importante en el aumento de la regeneración de heridas de la manifestación oral en el síndrome respiratorio agudo severo coronavirus 2 (SARS-CoV-2) como se documenta in silico.

Palabras Clave: COVID-19; enfermedad infecciosa; Hibiscus sabdariffa; medicamento; odontología.

Citation Format: Ramadhani NF, Nugraha AP, Rahmadani D, Puspitaningrum MS, Rizqianti Y, Kharisma VD, Noor TNEBTA, Ridwan RD, Ernawati DS, Nugraha AP (2022) Anthocyanin, tartaric acid, ascorbic acid of roselle flower (Hibiscus sabdariffa L.) for immunomodulatory adjuvant therapy in oral manifestation coronavirus disease-19: An immunoinformatic approach. J Pharm Pharmacogn Res 10(3): 418–428. https://doi.org/10.56499/jppres21.1316_10.3.418

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Moroccan medicinal plants against COVID-19

November 6, 2021Pharmaceutical ScienceCOVID-19, ethnomedicine, medicinal plants, molecular docking, Morocco, SARS-CoV-2jppres

J Pharm Pharmacogn Res 10(2): 227-238, 2022.

DOI: https://doi.org/10.56499/jppres21.1200_10.2.227

Original Article

Molecular docking study of the main phytochemicals of some medicinal plants used against COVID-19 by the rural population of Al-Haouz region, Morocco

[Estudio de acoplamiento molecular de los principales fitoquímicos de algunas plantas medicinales utilizadas contra el COVID-19 por la población rural de la región de Al-Haouz, Marruecos]

Ridwane Ghanimi¹*, Ahmed Ouhammou², Yassine El Atki³, Mohamed Cherkaoui¹

¹Laboratory of Pharmacology, Neurobiology, Anthropobiology, Environment and Behaviour, Department of Biology, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, BP 2390, 40000, Morocco.

²Laboratory of Microbial Biotechnologies, Agrosciences and Environment (BioMAgE), Agrosciences, Phytobiodiversity and Environment Team, Regional Herbarium ‘MARK’, Department of Biology, Faculty of Sciences Semlalia , Cadi Ayyad University, PO. Box 2390, Marrakech, 400001, Morocco.

³Laboratory of Physiology Pharmacology and Environmental Health, Department of Biology, Faculty of Sciences Dhar Mehraz,Sidi Mohamed Ben Abdellah University, Fez, Morocco.

*E-mail: ghanimiridwane@gmail.com, ridwane.ghanimi@ced.uca.ma

Abstract

Context: The infection by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a global health emergency. The management of this crisis requires the discovery of new drugs able to cure or reduce the severity of SARS-CoV-2.

Aims: To explore the medicinal plants consumed by the rural population of Al-Haouz region against the emergence of the COVID-19, and to assess in silico the main phytochemicals present in the essential oils and the extracts of these medicinal plants, as potential inhibitors of the COVID-19 main protease (M^pro).

Methods: The survey was conducted through a semi-structured questionnaire among 85 respondents aged 30 years and above, in the Al-Haouz region, Morocco. AutoDock Vina, was used to assess the binding affinity of the phytochemicals to the M^pro.

Results: Eleven wild medicinal species were cited; 10 belonging to the Lamiaceae family and one to the Compositae family. Thymus saturejoides Coss., Artemisia herba-alba Asso.and Mentha suaveolens Ehrh. were respectively the three most cited species during the survey. The rosmarinic acid (-7.7 kcal/mol), hesperetin (-7.2 kcal/mol), gallocatechin (-7.2 kcal/mol) and cyasterone (-7.2 kcal/mol) have shown the higher inhibitory potential against covid-19 M^pro respectively.

Conclusions: In addition to their different recognized biological activities, the medicinal plants used in the Al-Haouz region have shown good inhibitory potential against SARAS-CoV-2 M^pro. Furthermore, the phytochemicals that exhibited the highest inhibitory potentials in this virtual study require further investigation in vitro and in vivo.

Keywords: COVID-19; ethnomedicine; medicinal plants; molecular docking; Morocco; SARS-CoV-2.

Resumen

Contexto: La infección por el coronavirus 2 del síndrome respiratorio agudo severo (SARS-CoV-2) es una emergencia sanitaria mundial. El manejo de esta crisis requiere el descubrimiento de nuevos medicamentos capaces de curar o reducir la gravedad del SARS-CoV-2.

Objetivos: Explorar las plantas medicinales consumidas por la población rural de la región de Al-Haouz frente a la aparición del COVID-19, y evaluar in silico los principales fitoquímicos presentes en los aceites esenciales y los extractos de estas plantas medicinales, como potenciales inhibidores. de la proteasa principal COVID-19 (M^pro).

Métodos: La encuesta se realizó a través de un cuestionario semiestructurado entre 85 encuestados de 30 años o más, en la región de Al-haouz, Marruecos. Se utilizó AutoDock Vina para evaluar la afinidad de unión de los fitoquímicos al M^pro.

Resultados: Se citaron once especies medicinales silvestres; 10 pertenecientes a la familia Lamiaceae y una a la familia Compositae. Thymus saturejoides Coss., Artemisia herba-alba Asso. y Mentha suaveolens Ehrh. fueron, respectivamente, las tres especies más citadas durante la encuesta. El ácido rosmarínico (-7,7 kcal/mol), la hesperetina (-7,2 kcal/mol), la galocatequina (-7,2 kcal/mol) y la ciasterona (-7,2 kcal/mol) han mostrado el mayor potencial inhibitorio frente al covid-19 M^pro, respectivamente.

Conclusiones: Además de sus diferentes actividades biológicas reconocidas, las plantas medicinales utilizadas en la región de Al-Haouz han mostrado un buen potencial inhibitorio contra SARAS-CoV-2 M^pro. Además, los fitoquímicos que exhibieron los potenciales inhibidores más altos en este estudio virtual requieren más investigación in vitro e in vivo.

Palabras Clave: acoplamiento molecular; COVID-19; etnomedicina; Marruecos; plantas medicinales; SARS-CoV-2.

Citation Format: Ghanimi R, Ouhammou A, El Atki Y, Cherkaoui M (2022) Molecular docking study of the main phytochemicals of some medicinal plants used against COVID-19 by the rural population of Al-Haouz region, Morocco. J Pharm Pharmacogn Res 10(2): 227–238. https://doi.org/10.56499/jppres21.1200_10.2.227

Volume 9, Suppl. 1 (MICPS 2021)

October 11, 2021Pharmaceutical Scienceantioxidant, antioxidant activity, apoptosis, COVID-19, cytotoxicity, inflammation, medicinal plant, molecular docking, pharmaceutical sciences, pharmacology, pharmacy, SARS-CoV-2jppres

J Pharm Pharmacogn Res 9(Suppl. 1), (October) 2021

1st Makassar International Conference on Pharmaceutical Sciences

(MICPS 2021)

Empowering Natural Product in Drugs Discovery and Development

Faculty of Pharmacy Universitas Muslim Indonesia

Makassar, Indonesia

September 25-26, 2021

Conference Proceedings [1.3 Mb]

Editing, design and realization: Gabino Garrido, Marisela Valdés, Xavier Garrido, Muammar Fawwaz, Aktsar Roskiana Ahmad

Editorial Scientific Council: Muammar Fawwaz, Aktsar Roskiana Ahmad, A. Emelda, Nurmaya Effendi

Phaleria macrocarpa as anti-breast cancer agent

June 30, 2021Pharmaceutical Scienceanticancer activity, binding affinity, bioactive compound, molecular docking, Phaleria macrocarpajppres

J Pharm Pharmacogn Res 9(6): 824-845, 2021.

Original article

Anti-breast cancer potential activity of Phaleria macrocarpa (Scheff.) Boerl.leaf extract through in silico studies

[Potencial actividad contra el cáncer de mama del extracto de hoja de Phaleria macrocarpa (Scheff.) Boerl. mediante estudios in silico]

Yuyun Ika Christina¹, Wirdatun Nafisah², Mochammad Fitri Atho’illah², Muhaimin Rifa’i², Nashi Widodo², Muhammad Sasmito Djati²*

¹Doctoral Program, Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang 65145, East Java, Indonesia.

²Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang 65145, East Java, Indonesia.

*E-mail: msdjati@ub.ac.id

Abstract

Context: The development of apoptotic agent from natural plant products may have a beneficial effect as a promising candidate for cancer therapy. The study about the efficacy of Phaleria macrocarpa leaves on breast cancer is still limited.

Aims: To elucidate the molecular mechanisms underlying the anti-breast cancer activity of P. macrocarpa leaves extract by in silico analysis.

Methods: The compounds of the ethanol extract of P. macrocarpa were identified by Liquid Chromatography–High Resolution Mass Spectrometry (LC-HRMS) analysis. Fourteen bioactive compounds of P. macrocarpa leaf were analyzed to determine the biological activity using Prediction of Activity Spectra for Substances (PASS) server. The network analysis was analyzed using STRING (https://string-db.org/). Twelve selected compounds were docked with several protein targets, including caspase 3, Bax and Bcl-2. Molecular docking was done by Pyrx 0.8 software and visualized by Discovery Studio software. The pharmacological properties of investigated bioactive compounds were analyzed using the SwissADME web server.

Results: The twelve from fourteen bioactive compounds of P. macrocarpa leaf have anticancer properties and might be expected to involve in p53 and PI3K/Akt signaling pathways related to cancer. The molecular docking result showed that sesamin from the lignans group has the best binding affinity to caspase-3 and Bax. Meanwhile, corymboside from the flavonoid group has the best binding affinity to Bcl-2.

Conclusions: The bioactive compounds of P. macrocarpa leaves extract might potentially modulate apoptosis and cell growth. Further research should be performed to validate the activity of P. macrocarpa bioactive compounds for target cancer development.

Keywords: anticancer activity; binding affinity; bioactive compound; molecular docking; Phaleria macrocarpa.

Resumen

Contexto: El desarrollo de un agente apoptótico a partir de productos vegetales naturales puede tener un efecto beneficioso como candidato prometedor para la terapia del cáncer. El estudio sobre la eficacia de las hojas de Phaleria macrocarpa en el cáncer de mama aún es limitado.

Objetivos: Dilucidar los mecanismos moleculares que subyacen a la actividad anticancerígena del extracto de hojas de P. macrocarpa mediante análisis in silico.

Métodos: Los compuestos del extracto etanólico de P. macrocarpa se identificaron mediante análisis de cromatografía líquida-espectrometría de masas de alta resolución (LC-HRMS). Catorce compuestos bioactivos de la hoja de P. macrocarpa fueron analizados para determinar la actividad biológica utilizando el servidor de Predicción de Espectros de Actividad para Sustancias (PASS). El análisis de la red se analizó utilizando STRING (https://string-db.org/). Se acoplaron doce compuestos seleccionados con varias dianas proteicas, incluida la caspasa 3, Bax y Bcl-2. El acoplamiento molecular se realizó con el software Pyrx 0.8 y se visualizó con el software Discovery Studio. Las propiedades farmacológicas de los compuestos bioactivos investigados se analizaron utilizando el servidor web SwissADME.

Resultados: Doce de los catorce compuestos bioactivos de la hoja de P. macrocarpa tienen propiedades anticancerígenas y se puede esperar que participen en las vías de señalización de p53 y PI3K/Akt relacionadas con el cáncer. El resultado del acoplamiento molecular mostró que la sesamina del grupo de los lignanos tiene la mejor afinidad de unión a la caspasa-3 y Bax. Mientras tanto, el corimbósido del grupo flavonoide tiene la mejor afinidad de unión a Bcl-2.

Conclusiones: Los compuestos bioactivos del extracto de hojas de P. macrocarpa podrían potencialmente modular la apoptosis y el crecimiento celular. Se deben realizar más investigaciones para validar la actividad de los compuestos bioactivos de P. macrocarpa para el desarrollo de dianas terapéuticas contra el cáncer.

Palabras Clave: acoplamiento molecular; actividad anticancerígena; afinidad de unión; compuesto bioactivo; Phaleria macrocarpa.

Citation Format: Christina YI, Nafisah W, Atho'illah MF, Rifa'i M, Widodo N, Djati MS (2021) Anti-breast cancer potential activity of Phaleria macrocarpa (Scheff.) Boerl. leaf extract through in silico studies. J Pharm Pharmacogn Res 9(6): 824–845.

Potential of polyether ionophore compounds as antimalarials through inhibition on Plasmodium falciparum glutathione S-transferase by molecular docking studies

[Potencial de los compuestos ionóforos de poliéter como antimaláricos mediante la inhibición de glutatión S-transferasa de Plasmodium falciparum a través de estudios de acoplamiento molecular]

Alfian Wika Cahyono1,2, Icha Farihah Deniyati Faratisha1, Nabila Erina Erwan1,3, Rivo Yudhinata Brian Nugraha1,4, Ajeng Maharani Putri1,3, Loeki Enggar Fitri1,4*

Resumen

References

Molecular simulation of compounds from n-hexane fraction of Sonchus arvensis L. leaves as SARS-CoV-2 antiviral through inhibitor activity targeting strategic viral protein

[Simulación molecular de compuestos de la fracción de n-hexano de las hojas de Sonchus arvensis L. como antivirales del SARS-CoV-2 a través de la actividad inhibidora dirigida a la proteína viral estratégica]

Dwi Kusuma Wahyuni1,2*, Sumrit Wacharasindhu3, Wichanee Bankeeree2, Hunsa Punnapayak2, Hery Purnobasuki1, Junairiah1, Arif NM Ansori4, Viol Dhea Kharisma1,5, Arli Aditya Parikesit6, Listyani Suhargo1*, Sehanat Prasongsuk1,2*

Resumen

References

In silico analysis of anti-dengue activity of faloak (Sterculia quadrifida R. Br) stem bark compounds

[Análisis in silico de la actividad anti-dengue de compuestos de corteza de tallo de faloak (Sterculia quadrifida R. Br.)]

Audrey G. Riwu1, Jusak Nugraha2, Djoko A. Purwanto3*, Erwin A. Triyono4

Resumen

References

Anti-inflammatory and antioxidant potential of Syzygium polyanthum (Wight) Walp. bioactive compounds in polycystic ovary syndrome: An in silico study

[Potencial anti-inflamatorio y antioxidante de compuestos bioactivos de Syzygium polyanthum (Wight) Walp. en el síndrome de ovario poliquístico: Un estudio in silico]

Renny Aditya1,4, Budi Santoso2*, Widjiati Widjiati3

Abstract

Resumen

References

Flavonoids as potential inhibitors of dengue virus 2 (DENV2) envelope protein

[Flavonoides como posibles inhibidores de la proteína de la cubierta del virus del dengue 2 (DENV2)]

Rachel Raditya Renantha1, Alvin Richardo Liga1, Christy Bianca Tanugroho1, Lovine Xaviera Denovian1, Siti Lateefa Az Zahra Budiyanto2, Arli Aditya Parikesit2*

Abstract

Resumen

References

Volatile compounds from Phyla scaberrima (Juss. ex Pers.) Moldenke and Dysphania ambrosioides (L.) Mosyakin & Clemants as possible SARS-CoV-2 protease inhibitors: Identification and in-silico study

[Compuestos volátiles de Phyla scaberrima (Juss. ex Pers.) Moldenke y Dysphania ambrosioides (L.) Mosyakin & Clemants como posibles inhibidores de proteasas de SARS-CoV-2: Identificación y estudio in-silico]

Neyder Contreras-Puentes1*, Manuel Salas-Moreno2,3, Lina Mosquera-Chaverra2, Leonomir Córdoba-Tovar4, Antistio Alviz-Amador5

Abstract

Resumen

References

Anthocyanin, tartaric acid, ascorbic acid of roselle flower (Hibiscus sabdariffa L.) for immunomodulatory adjuvant therapy in oral manifestation coronavirus disease-19: An immunoinformatic approach

[Antocianina, ácido tartárico, ácido ascórbico de flor de Jamaica (Hibiscus sabdariffa L.) para la terapia adyuvante inmunomoduladora en la manifestación oral de la enfermedad por coronavirus-19: Un enfoque inmunoinformático]

Nastiti Faradilla Ramadhani1, Alexander Patera Nugraha1,2*, Desintya Rahmadhani3, Martining Shoffa Puspitaningrum3, Yuniar Rizqianti3, Viol Dhea Kharisma4, Tengku Natasha Eleena binti Tengku Ahmad Noor5, Rini Devijanti Ridwan6, Diah Savitri Ernawati7, Albertus Putera Nugraha8

Abstract

Resumen

References

J Pharm Pharmacogn Res 10(2): 227-238, 2022.

Original Article

Molecular docking study of the main phytochemicals of some medicinal plants used against COVID-19 by the rural population of Al-Haouz region, Morocco

[Estudio de acoplamiento molecular de los principales fitoquímicos de algunas plantas medicinales utilizadas contra el COVID-19 por la población rural de la región de Al-Haouz, Marruecos]

Ridwane Ghanimi1*, Ahmed Ouhammou2, Yassine El Atki3, Mohamed Cherkaoui1

Resumen

1st Makassar International Conference on Pharmaceutical Sciences

(MICPS 2021)

Conference Proceedings [1.3 Mb]

Editing, design and realization: Gabino Garrido, Marisela Valdés, Xavier Garrido, Muammar Fawwaz, Aktsar Roskiana Ahmad

Editorial Scientific Council: Muammar Fawwaz, Aktsar Roskiana Ahmad, A. Emelda, Nurmaya Effendi

J Pharm Pharmacogn Res 9(6): 824-845, 2021.

Original article

Anti-breast cancer potential activity of Phaleria macrocarpa (Scheff.) Boerl.leaf extract through in silico studies

[Potencial actividad contra el cáncer de mama del extracto de hoja de Phaleria macrocarpa (Scheff.) Boerl. mediante estudios in silico]

Yuyun Ika Christina 1, Wirdatun Nafisah2, Mochammad Fitri Atho’illah2, Muhaimin Rifa’i2, Nashi Widodo2, Muhammad Sasmito Djati2*

Abstract

Resumen

Alfian Wika Cahyono^1,2, Icha Farihah Deniyati Faratisha¹, Nabila Erina Erwan^1,3, Rivo Yudhinata Brian Nugraha^1,4, Ajeng Maharani Putri^1,3, Loeki Enggar Fitri^1,4*

Dwi Kusuma Wahyuni^1,2, Sumrit Wacharasindhu³, Wichanee Bankeeree², Hunsa Punnapayak², Hery Purnobasuki¹, Junairiah¹, Arif NM Ansori⁴, Viol Dhea Kharisma^1,5, Arli Aditya Parikesit⁶, Listyani Suhargo¹, Sehanat Prasongsuk^1,2*

Audrey G. Riwu¹, Jusak Nugraha², Djoko A. Purwanto^3*, Erwin A. Triyono⁴

Renny Aditya^1,4, Budi Santoso²*, Widjiati Widjiati³

Rachel Raditya Renantha¹, Alvin Richardo Liga¹, Christy Bianca Tanugroho¹, Lovine Xaviera Denovian¹, Siti Lateefa Az Zahra Budiyanto², Arli Aditya Parikesit^2*

Neyder Contreras-Puentes^1*, Manuel Salas-Moreno^2,3, Lina Mosquera-Chaverra², Leonomir Córdoba-Tovar⁴, Antistio Alviz-Amador⁵

Nastiti Faradilla Ramadhani¹, Alexander Patera Nugraha^1,2*, Desintya Rahmadhani³, Martining Shoffa Puspitaningrum³, Yuniar Rizqianti³, Viol Dhea Kharisma⁴, Tengku Natasha Eleena binti Tengku Ahmad Noor⁵, Rini Devijanti Ridwan⁶, Diah Savitri Ernawati⁷, Albertus Putera Nugraha⁸

Ridwane Ghanimi¹*, Ahmed Ouhammou², Yassine El Atki³, Mohamed Cherkaoui¹

Yuyun Ika Christina¹, Wirdatun Nafisah², Mochammad Fitri Atho’illah², Muhaimin Rifa’i², Nashi Widodo², Muhammad Sasmito Djati²*