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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Biotropika The Journal of Pure and Applied Chemistry Research Jurnal Ternak Tropika Journal of Tropical Biodiversity and Biotechnology Indonesian Journal of Chemistry JSMARTech : Journal of Smart Bioprospecting and Technology Berkala Penelitian Hayati Makara Journal of Science
Hermanto, Feri Eko
Department Of Biology, Faculty Of Mathematics And Natural Sciences, Brawijaya University, Indonesia; Science Bridge Indonesia, Department Of Biology, Faculty Of Mathematics And Natural Sciences, Brawijaya University, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Environmental Science Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience

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Anti-Obesity Properties of Black Pepper (Piper nigrum): Completing Puzzle using Computational Analysis Lailiyah, Nurun Nafi'atul; Ibrahim, Mutiara Dwirosita; Fitriani, Chunafa Ayu; Hermanto, Feri Eko
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 3 (2021)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.03.101

Abstract

Pepper (Piper nigrum) is one of the most common spices found in almost every food. Current knowledge informed that pepper regulates physiological activity in obesity. However, the exact mechanism is still poorly understood. This study determined the potential of piperine and piperidine as major compounds in pepper as GHSR-Ghrelin inhibitors due to over-activity of Ghrelin as appetite hormone in obesity. Molecular docking was performed to simulate the binding pattern of piperine and piperidine as GHSR-Ghrelin antagonist. The result showed that piperidine has a lower potential as GHSR-Ghrelin antagonist than piperine based on binding energy calculation and amino acid interaction. Further, piperine binding to GHSR could shift the Ghrelin binding site to the GHSR. In conclusion, piperine may act as an inhibitor of GHSR-Ghrelin interaction to prevent appetite behavior resulting in bodyweight loss in obesity.  
Virtual prediction of antiviral potential of ginger (Zingiber officinale) bioactive compounds against spike and MPro of SARS-CoV2 protein Ahmad Hafidul Ahkam; Feri Eko Hermanto; Adzral Alamsyah; Iva Himmatul Aliyyah; Fatchiyah Fatchiyah
JURNAL PENELITIAN BIOLOGI BERKALA PENELITIAN HAYATI Vol 25 No 2 (2020): June 2020
Publisher : The East Java Biological Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (33.627 KB) | DOI: 10.23869/50

Abstract

Coronavirus disease 2019 (COVID-19) is a human disease caused by SARS-CoV2 becomes a serious health threat after infected more than 6 million people globally. The virus enters the host cell through an S protein on its surface and begins its life cycle with the help of a key protein, MPro. On the other hand, several bioactive from Ginger have been reported for their antiviral properties, but few studies related to COVID-19. This study aims to evaluate the potential of a few bioactive compounds from Ginger as anti-SARS-CoV2. Gingerenone A, gingerol, geraniol, shogaol, zingiberene, zingiberenol, and zingerone were used as ligand to be docked with S protein and MPro. Drug-likeness properties also evaluated using SwissADME. Gingerenone A constantly gave the lowest binding energy compared to others both with S or MPro. However, gingerol, geraniol, shogaol, zingiberene, zingiberenol, and zingerone could interact with key residues responsible for MPro catalytic domain, while geraniol, shogaol, zingiberene, zingiberenol, and zingerone could interfere S-ACE2 binding shape and increase its binding energy. The drug-likeness analysis also revealed that all of the analyzed compounds have no violation of Lipinski’s Rule of 5. In conclusion, gingerol, geraniol, shogaol, zingiberene, zingiberenol, and zingerone from Ginger have good potential as antiviral agents with good oral bioavailability and flexibility
Molecular biology education in Indonesia - suggestions for improvement Wolfgang Nellen; Atika Hanoum Rahasta; Feri Eko Hermanto; Margareth Rika Wahyusari Gabriella Lorenza
JURNAL PENELITIAN BIOLOGI BERKALA PENELITIAN HAYATI Vol 22 No 2 (2017): June 2017
Publisher : The East Java Biological Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (825.118 KB) | DOI: 10.23869/59

Abstract

Education in molecular biology is considered difficult because it is complex and requires a lot of basic knowledge. Focused on basic science facts, it is usually taught with little connection to everyday life. A second problem is that the topic is rather abstract and results are only indirectly observed: we know that DNA is a double helix - but nobody has seen it directly. In contrast to subjects in the humanities and social sciences, molecular biology is a handy-craft where sophisticated theory and practical lab-work go hand in hand. Molecular biology is not so much a specific sub-discipline of biosciences but rather a huge tool box which is indispensable for all other fields of biology. It is therefore absolutely required for all biologists to know the basics and the potential of molecular biology in their specific field of interest. We present some thoughts how to make the theory more attractive, how to combine learning, training and teaching of theory and practice, how to stimulate independent, critical thinking in students and final-ly, how to identify and support excellent students who should advance science in the next generation. Last not least, we emphasize the necessity to expand information and teaching of molecular biology to the public.
Novel Antimalarial Drug Screening Based on Methyl Eugenol, Cinnamaldehyde, and Thiosemicarbazone with Cysteine Protease Inhibition: In Silico Molecular Docking, Molecular Dynamics, and ADMET Studies Lucy Arianie; Feri Eko Hermanto; Elvina Dhiaul Iftitah; Warsito Warsito; Widodo Widodo
The Journal of Pure and Applied Chemistry Research Vol 11, No 2 (2022): Edition May-August 2022
Publisher : Chemistry Department, The University of Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jpacr.2022.011.02.652

Abstract

Plasmodium falciparum malaria contributes to significant global diseases. Computer-aided drug design, screening, and discovery were used to analyze a novel series of Methyl Eugenol Benzaldehyde Thiosemicarbazone (MEBThi) and Methyl Eugenol Cinnamaldehyde Thiosemicarbazone (MECThi) derivatives for malaria falciparum inhibition. This present study showed that 16 molecules from 28 of MEBThi and MECThi have affinities and interaction with active-site residues of cysteine protease, a key player in erythrocyte proliferation of P. falciparum. 13-MECThi demonstrates the best binding affinity at ˗8.0 kcal/mol while co-drug ˗5.6 kcal/mol. Physicochemical and pharmacokinetic assays of 13- MECThi have also revealed this potent compound. Toxicity analysis shows that 13-MECThi does not have mutagenicity and carcinogenicity characters, whereas co-drug has mutagenicity probability. The molecular dynamic evaluation illustrated that the 13-MECThi complex has higher Root Mean Square Deviation (RMSD) values, indicating its structure was more flexible than the chloroquine complex. Root Mean Square Fluctuation (RMSF) complex of receptor and 13-MECThi has no fundamental differences with chloroquine complex. This designed compound should be considered a falciparum antimalarial drug.
On the Hypolipidemic Activity of Elicited Soybeans: Evidences Based on Computational Analysis Feri Eko Hermanto; Warsito Warsito; Muhaimin Rifa'i; Nashi Widodo
Indonesian Journal of Chemistry Vol 22, No 6 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.75777

Abstract

Dietary intervention plays a significant role in regulating hyperlipidemia. Besides, elicited soybean has greater bioactive contents with numerous health benefits potential. However, there is no evidence of the hypolipidemic activity of elicited soybean. This study will explore the potential mechanism of hypolipidemic activity of bioactive compounds from elicited soybean through computational modeling. The phytocompounds from elicited soybean were identified by Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS), then screened for potential toxicity and drug-likeness properties. Compounds with low potential toxicity and excellent drug-likeness properties were screened for hypolipidemic activity against 3-Hydroxy-3-Methylglutaryl-CoA Reductase (HMGCR) and Peroxisome Proliferator Activator Receptor-gamma (PPAR-γ) through molecular docking coupled with molecular dynamics. The result showed that phytocompounds from the isoflavonoid group have an excellent affinity to bind with the HMGCR and PPAR-γ. Daidzein, Genistein, and Glycitein interacted with the catalytic residues of HMGCR to act as potential inhibitors with great affinity and stability. Genistein and Glycitein showed strong affinity and stability during their interaction with the agonistic sites of PPAR-γ. Further, the protein network described that targeting HMGCR inhibitor and PPAR-γ had the advantage in orchestrating cholesterol metabolism homeostasis. In summary, isoflavonoids from elicited soybean may have hypolipidemic activity through HMGCR inhibition and PPAR-γ activation.
Nutritional Contents and Bioactive Compounds among Several Variants of Dolichos lablab: Fundamental Facts for Functional Food Development Elly Purwanti; Feri Eko Hermanto; Wahyu Prihanta; Tutut Indria Permana; I Gusti Ngurah Agung Wiwekananda
Journal of Tropical Biodiversity and Biotechnology Vol 8, No 2 (2023): August
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.81339

Abstract

To date, the data describing various nutritional and secondary metabolites content of Lablab beans is incomplete. Therefore, this study evaluated the nutritional value, secondary metabolites, and antioxidant activity of three different variants of Lablab beans, i.e., brown, black, and cream beans. The results showed that the brown Lablab beans had outperformed other variants according to their nutritional value and flavonoid content with outstanding DPPH scavenging activity. However, the black beans also showed good bioactive contents through their total phenolic percentage with decent reducing activity via the FRAP assay. Those who are keen in developing functional food from Lablab beans should consider this data as a reference. 
Pro-Apoptosis Activity of Pogostemon cablin Benth. Against Nasopharyngeal Carcinoma through the BCL-2 Inhibition Signaling Pathway: A Computational Investigation Syahraini, Aigia; Harnelly, Essy; Hermanto, Feri Eko
Makara Journal of Science Vol. 27, No. 3
Publisher : UI Scholars Hub

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Resistance to chemotherapy and radiotherapy frequently emerges in the later stage of nasopharyngeal carcinoma (NPC) tumorigenesis. The decreased response of NPC to radiotherapy and chemotherapy occurs owing to the inhibition of cancer cell apoptosis by the B-cell lymphoma-2 (BCL-2) protein. Thus, inhibiting BCL-2 protein may become a powerful approach to eliminate NPC through apoptosis regulation. Meanwhile, Pogostemon cablin is reported to exhibit anticancer properties, but there are limited studies on its use for NPC treatment. The objective of this study is to investigate the potential bioactive compounds in P. cablin as anti-apoptosis BCL-2 protein inhibitors using in-silico approach. Natural compounds from P. cablin were retrieved from the KNApSAcK database and screened for inhibitory effects on BCL-2 protein via molecular docking coupled with molecular dynamics. It was found that apigenin, rhamnetin, and apigenin 7-(6″-p coumarylglucoside) showed potential inhibitory properties against BCL-2 protein based on binding affinity and interaction chemistry. The highest binding affinity was recorded for apigenin 7-(6″-p coumarylglucoside) at −9.9 kcal/mol, followed by rhamnetin and apigenin at −7.2 kcal/mol. These compounds are also bound to the inhibitory sites of BCL-2 and venetoclax, mainly by hydrophobic bonds and Van der Waals interactions. Nevertheless, molecular dynamics simulations revealed that apigenin 7-(6″-p-coumarylglucoside) had unstable conformation and binding to BCL-2. In summary, this study demonstrated that P. cablin has excellent potency as an alternative or complementary therapy against radiotherapy and chemotherapy resistance of NPC, mainly through rhamnetin and apigenin.
Chrysin Inhibits Indonesian Serotype Foot-and-Mouth-Disease Virus Replication: Insights from DFT, Molecular Docking and Dynamics Analyses Susilo, Agus; Cahyati, Miftakhul; Nurjannah, Nurjannah; Pranowo, Dodyk; Hermanto, Feri Eko; Primandasari, Elma Putri
Journal of Tropical Biodiversity and Biotechnology Vol 9, No 1 (2024): March
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jtbb.83140

Abstract

Chrysin, a predominant compound in Propolis, possesses diverse bioactivities, including antiviral properties. However, its antiviral efficacy against the Indonesian Foot-and-Mouth Disease Virus (FMDV) serotype remains unexplored. This study investigates Chrysin's inhibitory potential against FMDV Indonesian serotype by targeting the 3C Protease (3CP), a vital enzyme for viral replication. Multiple sequence alignment was used to reveal unique characteristics of the Indonesian serotype's 3CP compared to global serotypes. Density Functional Theory (DFT) calculations assessed Chrysin's interaction with 3CP based on electronegativity. Molecular docking and molecular dynamics analyses evaluated Chrysin's inhibitory activity against 3CP, using homology modeling for the Indonesian serotype's 3CP structure. Luteolin, a known FMDV 3CP inhibitor with a similar structure to Chrysin, served as a reference. Results showed distinct 3CP sequences in the Indonesian serotype compared to O serotypes and others. Chrysin exhibited potential electron-donor activity with lower HOMO and LUMO values than Luteolin, but they had similar energy gaps, i.e., 4.016 and 4.044 eV, respectively. Molecular docking indicated similar binding affinities, with Chrysin (-6.365 kcal/mol) and Luteolin (-6.864 kcal/mol) bound to active site residues. Molecular dynamics analysis demonstrated stable 3CP-Chrysin and 3CP-Luteolin complexes, with minor differences in Radius of gyration (Rg) and Root-Mean-Square Fluctuation (RMSF) below 1 Å. From the ligand stability point of view, Chrysin had comparable stability with Luteolin. However, Chrysin formed fewer hydrogen bonds and displayed greater free-binding energy than Luteolin during simulation periods. These findings suggest that Chrysin holds promise as an inhibitor of the Indonesian serotype's FMDV 3C Protease. 
Computational Insight on Bioactive Compound Potential Activity of Kenitu (Chrysophyllum cainito L.) Leaves as PPAR-y Antagonist for Obesity Rosyada, Nabila Nur; Andyni, Regina Shania; Alvionita, Cicin Vinolia; Narwasthu, Sekararum; Adawiyah, Robiatul; Hermanto, Feri Eko; Kurniawan, Nia; Fatchiyah, Fatchiyah
Biotropika: Journal of Tropical Biology Vol. 12 No. 2 (2024)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2024.012.02.03

Abstract

Studies reported that kenitu (Chrysophyllum cainito) has the potential as an anti-obesity agent. However, the mechanism underlying that activity remains unknown. On the other hand, targeting PPAR-y has played a beneficial role in regulating obesity. Therefore, this study will explain the anti-obesity potential of natural compounds from C. cainito in modulating obesity through inhibition of PPAR-y. Molecular docking was employed to identify the possibility of several compounds binding with the PPAR-y. Moreover, the stability of the interaction between PPAR-y and each compound was also evaluated using molecular dynamics analysis. The result showed that beta-sitosterol, lupeol, myricitrin, quercitrin, rutin, vitamin A, epicatechin, and chlorogenic acid are worthy of potential as PPAR-y antagonists. In advance, molecular dynamics simulations revealed that chlorogenic acid, quercitrin, and epicatechin were the most stable compounds to interact as an inhibitor of PPAR-y. In conclusion, compounds from star apple have some potential to improve the health status of patients’ obesity through PPAR-y antagonist activity.
Pengaruh Pemberian Feed Additive Ekstrak Nano Cair Jahe, Kunyit, Daun Jati dan Probiotik Terhadap Persentase Karkas dan Kualitas Fisik Daging Ayam Broiler Nuningtyas, Yuli Frita; Natsir, Muhammad Halim; Hermanto, Feri Eko; Marwi, Filoza; Fionita, Rina Aqila
TERNAK TROPIKA Journal of Tropical Animal Production Vol. 25 No. 1 (2024): TERNAK TROPIKA Journal of Tropical Animal Production
Publisher : Jurusan Produksi Ternak, Fakultas Peternakan, Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jtapro.2024.025.01.10

Abstract

Tujuan dari penelitian ini adalah untuk mengevaluasi ekstrak jahe, kunyit dan daun jati dalam bentuk nano cair yang ditambahkan dengan probiotik pada pakan terhadap persentase karkas dan kualitas fisik daging ayam pedaging. Variabel yang diamati dalam penelitian ini adalah persentase karkas dan kualitas fisik daging yang meliputi kadar air, WHC (Water Holding Capacity), susut masak, keempukan, dan warna (L*, a*, b*). Penelitian dilakukan selama 35 hari secara in vivo. Penelitian ini menggunakan 200 ekor DOC ayam pedaging strain Lohmann dengan berat rata-rata 43,42 g ± 2,82 dan koefisien keragaman 6,48 %. Pakan dan minuman diberikan secara ad libitum. Metode yang digunakan adalah Rancangan Acak Lengkap (RAL) dengan 5 level perlakuan feed additive (0 %, 0,2 %, 0,4 %, 0,6 % dan 0,8 %) dimana setiap perlakuan terdiri dari 5 ulangan. Data yang diperoleh dianalisis dengan menggunakan analisis varians (ANOVA) dan apabila terdapat perbedaan nyata dilanjutkan dengan Uji Jarak Berganda Duncan (DMRT). Hasil penelitian bahwa pemberian feed additive ekstrak jahe, kunyit daun jati dan probiotik bentuk cair menunjukkan persentase karkas pada P4 sebesar 80,52 %, kadar air pada P4 68,17 %, WHC pada P3 45,33 %, susut masak pada P3 26,63 % keempukan pada P0 5,95 kg/cm2, warna L pada P2 51,93, a* pada P4 1,01 dan b* pada P4 6,90. Penambahan feed additive berupa ekstraksi jahe, kunyit, daun jati berbentuk nano cair dan probiotik level 0,4 – 0,8 % optimal dalam meningkatkan persentase karkas dan kualitas fisik daging (WHC, cooking loss, warna dan keempukan) pada ayam pedaging.
Co-Authors Adzral Alamsyah Agus Susilo Ahmad Hafidul Ahkam Alvionita, Cicin Vinolia Andyni, Regina Shania Atika Hanoum Rahasta Dinia Rizqi Dwijayanti Dodyk Pranowo Elly Purwanti Elvina Dhiaul Iftitah Essy Harnelly fatchiyah . Fionita, Rina Aqila Fitriani, Chunafa Ayu Grahadi, Rahmat I Gusti Ngurah Agung Wiwekananda Ibrahim, Mutiara Dwirosita Iva Himmatul Aliyyah Kamila, Fairuz Sarah Lailiyah, Nurun Nafi'atul Lucy Arianie Margareth Rika Wahyusari Gabriella Lorenza Marwi, Filoza Miftakhul Cahyati Muhaimin Rifa'i Muhammad Halim Natsir Narwasthu, Sekararum Nashi Widodo Nashi Widodo Nia Kurniawan Nurjannah Nurjannah Primandasari, Elma Putri Robiatul Adawiyah Rosyada, Nabila Nur Rosyadah, Nuraini Siti Mariyah Ulfa Syahraini, Aigia Tutut Indria Permana Wahyu Prihanta Warsito Warsito Widodo Widodo Widyananda, Muhammad Hermawan Wolfgang Nellen Yuli Frita Nuningtyas