@article {2104, title = {In Silico Study of Rhamnocitrin Extract from Clove Syzygium Aromaricum in Inhibiting Adenosine A1 Adenylate Cyclase Interaction}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {512-517}, type = {Original Article }, chapter = {512}, abstract = {

This study aims to analyze the potential of Rhamnocitrin, a compound found in clove extract (Syzygium aromaticum), as an inhibitor of Adenylate Cyclase through an in-silico approach. The research method involves the use of software such as Pymol, PyRx, Protein Plus, and Lipinski Rule for molecular interaction analysis and physicochemical characterization of Rhamnocitrin. The analysis results show that Rhamnocitrin has significant affinity towards Adenosine A1 with Binding Affinity values of -6.1, -5.8, and -5.7. RMSD analysis indicates good stability of the formed protein-ligand complexes, with RMSD values of 0, 3.129, and 3.696. Analysis using Protein Plus software reveals the interaction between Rhamnocitrin and Adenosine A1, while the lipinski analysis shows physicochemical characteristics of Rhamnocitrin that meet important criteria, such as a mass of 300, 3 hydrogen bond donors, 6 hydrogen bond acceptors, log P of 2.6, and molar reactivity of 77.27. These findings provide new insights into the development of potential therapies involving clove extract and Rhamnocitrin as inhibitors of Adenylate Cyclase, and further research is needed to validate their effectiveness and safety.

}, keywords = {Adenosine A1, Adenylate Cyclase inhibition, Molecular Docking., Rhamnocitrin, Syzygium aromaricum}, doi = {10.5530/pj.2023.15.111}, author = {Nita Yessirita and Rismi Verawati and Devi Purnamasari and Rollando Rollando and Riso Sari Mandeli and Muhammad Thoriq Albari and Putri Azhari and Rahadian Zainul and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {2063, title = {Interaction of Masilinic Acid from Clove Plant (Syzygium aromaticum) with CD81 Antigen in Inhibiting HIV Virus Regulation In Silico}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {484-488}, type = {Original Article }, chapter = {484}, abstract = {

This research explores the interaction of Masilinic Acid from the clove plant (Syzygium aromaticum) with the CD81 antigen to inhibit HIV virus regulation in silico. Using computational methods such as Pymol, Pyrex, and Protein Plus, we demonstrate that Masilinic Acid can significantly interact with the CD81 antigen. The obtained data shows binding affinities of -6.4, -6.2, and -5.7, and RMSD values of 0, 1.885, and 1.952. Further detailed interaction analysis with Protein Plus strengthens these findings, providing evidence of a strong interaction between Masilinic Acid and the CD81 antigen. This study also includes the testing of the Lepinski Rule of Five to assess the potential of Masilinic Acid as a drug candidate, with results indicating a mass of 472, three hydrogen bond donors, four hydrogen bond acceptors, a log P value of 6.2, and a molar reactivity of 134. These results indicate that Masilinic Acid has the potential as an inhibitor of the CD81-HIV interaction, which can be utilized as an effective antiviral strategy. Key words: Masilinic Acid, Clove plant, CD81 antigen, HIV virus, In silico.

}, keywords = {CD81 antigen, Clove plant, HIV virus, In Silico., Masilinic Acid}, doi = {10.5530/pj.2023.15.106}, author = {Rahadian Zainul and Elsa Yanuarti and Siti Amiroch and Muhammad Thoriq Albari and Rismi Verawati and Amalia Putri Lubis and AAA Murtadlo} } @article {2068, title = {Molecular Docking of Thaflavine from Camellia sinensis in Inhibiting B-Cell Lymphoma Through BCl2 Apoptosis Regulator: An In Silico Study}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {500-505}, type = {Original Article }, chapter = {500}, abstract = {

This study aims to analyze the potential of Thaflavine, a compound found in green tea (Camellia sinensis), as an inhibitor in inhibiting B-cell lymphoma through its interaction with the BCl2 apoptosis regulator using an in-silico approach. The research methodology involved the use of software tools such as PyMOL, PyRx, Protein Plus, and the Lepinski Rule. Through molecular docking analysis using PyMOL and PyRx, the findings of this study demonstrate significant interactions between Thaflavine and BCl2, with Binding Affinity values of -5.5, -4.6, and -4.6, and RMSD values of 0, 1.436, and 2.292. The analysis using Protein Plus indicates the presence of interactions between Thaflavine and BCl2. Additionally, the analysis using the Lepinski Rule of Five reveals that Thaflavine meets the criteria as a potential drug compound, with a molecular weight of 549, 9 hydrogen bond donors, 12 hydrogen bond acceptors, a log P value of -2.5, and a molar reactivity of 119.17. The findings of this study provide important contributions to the development of therapies for B-cell lymphoma through an in-silico approach. However, further research is needed for in vitro and in vivo validation.

}, keywords = {Apoptosis Regulator BCl2, B-cell Lymphoma, Camellia sinensis., In-Silico Thaflavine, Molecular docking}, doi = {10.5530/pj.2023.15.109}, author = {Rahadian Zainul and Rismi Verawati and Herland Satriawan and Teresa Liliana Wargasetia and Devi Purnamasari and Amalia Putri Lubis and Bahrun and Riso Sari Mandeli and Muhammad Thoriq Albari and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {1841, title = {Bioactive Compounds from Purslane (Portulaca oleracea L.) and Star Anise (Illicium verum Hook) as SARS-CoV-2 Antiviral Agent via Dual Inhibitor Mechanism: In Silico Approach}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {August 2022}, pages = {352-357}, type = {Original Article }, chapter = {352}, abstract = {

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the COVID-19 pandemic that infects humans and attacks the body{\textquoteright}s immune system. The purpose of the study was to identify the potential of bioactive compounds in purslane (Portulaca oleracea L.) and star anise (Illicium verum Hook) via a dual inhibitor mechanism against SARS-CoV-2 proteases with an in silico approach. The samples were obtained from PubChem and RSCB PDB. Antivirus probability prediction was performed on PASS Online. Virtual screening was performed with PyRx via molecular docking. Visualization was used by PyMol and Discovery Studio. Compounds with the best antiviral potential are indicated by the low binding affinity value to the target proteins, namely SARS-CoV-2 TMPRSS2 and PLpro. The results showed that purslane luteolin has the best antiviral potential. However, further studies are required to validate this computational prediction.

}, keywords = {Antiviral agent, Illicium verum Hook, in silico, Portulaca oleracea L., SARS-CoV-2}, doi = {10.5530/pj.2022.14.106}, author = {Nur Sofiatul Aini and Viol Dhea Kharisma and Muhammad Hermawan Widyananda and Ahmad Affan Ali Murtadlo and Rasyadan Taufiq Probojati and Dora Dayu Rahma Turista and Muhammad Badrut Tamam and Vikash Jakhmola and Dony Novaliendry and Riso Sari Mandeli and Budhi Oktavia and Muhammad Thoriq Albari and Saddam Al Aziz and Muhammad Raffi Ghifari and Okta Suryani and Putri Azhari and Muhammad Arya Ghifari and Devi Purnamasari and Agariadne Dwinggo Samala and Mirella Fonda Maahury and ANM Ansori and Rahadian Zainul} } @article {1873, title = {In Silico Screening of Bioactive Compounds from Garcinia mangostana L. Against SARS-CoV-2 via Tetra Inhibitors}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {October 2022}, pages = {575-579}, type = {Research Article}, chapter = {575}, abstract = {

The global COVID-19 pandemic caused by SARS-CoV-2 has been the resulted of massive human deaths since early 2020. The purpose of this study was to determine the potential of mangosteen (Garcinia mangostana L.) as an inhibitor of RBD spike, helicase, Mpro, and RdRp activity of SARS-CoV-2 with an in silico approach. The samples were obtained from PubChem and RCSB PDB. Analysis of the similarity of the drug was carried out with the Swiss ADME on the basis of Lipinski rule of five. Prediction of antivirus probabilities was carried out using PASS Online. Molecular screening was performed using PyRx through molecular docking. Discovery Studio was used for visualization. The bioactive compounds with the highest antiviral potential were indicated with the lowest binding affinity to the targeted proteins RBD spike, helicase, Mpro, and RdRp of SARS-CoV-2. The results indicated that mangiferin has the greatest potential as a potential antiviral. However, more research is required to validate the results of these computational predictions.

}, keywords = {Antiviral agent, Garcinia mangostana L., in silico, SARS-CoV-2}, doi = {10.5530/pj.2022.14.138}, author = {Nur Sofiatul Aini and Viol Dhea Kharisma and Muhammad Hermawan Widyananda and Ahmad Affan Ali Murtadlo and Rasyadan Taufiq Probojati and Dora Dayu Rahma Turista and Muhammad Badrut Tamam and Vikash Jakhmola and Elsa Yuniarti and Saddam Al Aziz and Muhammad Raffi Ghifari and Muhammad Thoriq Albari and Riso Sari Mandeli and Muhammad Arya Ghifari and Devi Purnamasari and Budhi Oktavia and Amalia Putri Lubis and Fajriah Azra and Fadhilah Fitri and ANM Ansori and Maksim Rebezov and Rahadian Zainul} } @article {1832, title = {In Silico Screening of Bioactive Compounds from Syzygium cumini L. and Moringa oleifera L. Against SARS-CoV-2 via Tetra Inhibitors}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {August 2022}, pages = {267-272}, type = {Original Article }, chapter = {267}, abstract = {

The global pandemic of COVID-19 has caused disastrous consequences for both humans and the economy. The purpose of this study was to determine the potential of juwet (Syzygium cumini L.) and moringa (Moringa oleifera L.) as inhibitors of RBD spike, helicase, Mpro, and RdRp activity of SARS-CoV-2 with an in-silico approach. Samples were obtained from PubChem and RSCB PDB databases. The drug similarity analysis was determined using Swiss ADME and the Lipinski rule of five. Prediction of antivirus probabilities is carried out with PASS Online. Molecular screening is performed by molecular docking using PyRx. Visualization was used using PyMol and Discovery Studio. The bioactive compounds with the best antiviral potential had the lowest affinity bonds to the target proteins against RBD spike, helicase, Mpro, and RdRp of SARS-CoV-2. Results show that ellagic acid from java plum and myricetin from moringa have the best potential as potential antivirals. However, more research is required to validate the results of these computational predictions.

}, keywords = {Antiviral agent, in silico, Moringa Oleifera L, SARS-CoV-2, Syzygium cumini L.}, doi = {10.5530/pj.2022.14.95}, author = {Nur Sofiatul Aini and Viol Dhea Kharisma and Muhammad Hermawan Widyananda and Ahmad Affan Ali Murtadlo and Rasyadan Taufiq Probojati and Dora Dayu Rahma Turista and Muhammad Badrut Tamam and Vikash Jakhmola and Devni Prima Sari and Muhammad Thoriq Albari and Devi Pernamasari and Muhammad Arya Ghifari and Muhammad Raffi Ghifari and Riso Sari Mandeli and Muhardi and Budhi Oktavia and Trisna Kumala Sari and Titi Sriwahyuni and Putri Azhari and Mirella Fonda Maahury and ANM Ansori and Rahadian Zainul} } @article {1872, title = {In Silico Study of Entry Inhibitor from Moringa oleifera Bioactive Compounds against SARS-CoV-2 Infection}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {October 2022}, pages = {565-574}, type = {Research Article}, chapter = {565}, abstract = {

The aim of this study is to screen the content of bioactive compounds of Moringa oleifera and to identify its potential as an antiviral against COVID 19 through an entry inhibitor mechanism using bioinformatics tools. The sample was obtained from PubChem database. Amino acis sequences were obtained from the NCBI. Protein modeling is made through the SWISSMODEL site. The target proteins for this study were SARS-CoV-2 Mpro and RdRp. The protein-inhibitory interaction of the drug from M. oleifera bioactive compounds to SARS-CoV-2 was predicted by molecular docking with PyRx software. The result shows that M. oleifera was a potential antiviral candidate for SARS-CoV-2 with an entry inhibitor mechanism through a compound, especially quercetin. The RFMS value of both interactions between Mpro and quercetion and RdRp with quercetin were not higher than 1.05. This result still needed further research to prove this prediction.

}, keywords = {Active site, COVID-19, Moringa oleifera, Mpro, RdRp}, doi = {10.5530/pj.2022.14.137}, author = {Nala Mawaddani and Ekris Sutiyanti and Muhammad Hermawan Widyananda and Viol Dhea Kharisma and Dora Dayu Rahma Turista and Muhammad Badrut Tamam and Vikash Jakhmola and Syamsurizal and Bayu Ramadhani Fajri and Muhammad Raffi Ghifari and Muhammad Thoriq Albari and Muhammad Arya Ghifari and Amalia Putri Lubis and Dony Novaliendry and Dwi Hilda Putri and Fadhilah Fitri and Devni Prima Sari and Alexander Patera Nugraha and ANM Ansori and Maksim Rebezov and Rahadian Zainul} } @article {1874, title = {The phytochemical and pharmacological activity of extract Kirinyuh (Chromolaena odorata L.) leaves: A Review}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {October 2022}, pages = {580-586}, type = {Research Article}, chapter = {580}, abstract = {

C. odorata L. is considered to be a plant weed that is scattered in various climates. As a weed, this plant contains a variety of beneficial secondary metabolites. Several studies have shown the benefits of C. odorata L. leaf extract. This study reviews the metabolite content and the pharmacological activities of C. odorata L. leaf extract. A literature search was carried out to obtain various studies related to the use of this plant extract. Secondary metabolites identified in C. odorata L. are alkaloids, flavonoids, tannins, saponins, and steroids. Several reports have also shown that even though it is considered a weed, C. odorata L. leaf extract also provides many benefits due to its pharmacological activities. Various pharmacological activities include anti-inflammatory, anti-microbial, antioxidant, antidyslipidemia, hematologic agent, antidiabetic and anti-cataract, analgesic and antipyretic, wound healing, anti-malaria, mosquito larvicidal, antihypercholesterolemia, and antifungal.

}, keywords = {Characterization, Chromolaena odorata, Kirinyuh, Pharmacological activity, Phytochemical}, doi = {10.5530/pj.2022.14.139}, author = {Erna Harfiani and Yudhi Nugraha and Citra Ayu Aprilia and Feda Anisah Makkiyah and Ratna Puspita and Viol Dhea Kharisma and Muhammad Hermawan Widyananda and Ahmad Affan Ali Murtadlo and Dora Dayu Rahma Turista and Muhammad Badrut Tamam and Riso Sari Mandeli and Mirella Fonda Maahury and Devi Purnamasari and Muhammad Arya Ghifari and Muhammad Thoriq Albari and Muhammad Raffi Ghifari and Asmi Citra Malina A. R. Tasakka and Alexander Patera Nugraha and Rahadian Zainul} } @article {1911, title = {The Potential of Antivirus Compounds in Gletang (Tridax procumbens Linn.) in Inhibiting 3CLpro Receptor of SARS-CoV-2 Virus by In Silico}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {December 2022}, pages = {796-805}, type = {Research Article }, chapter = {796}, abstract = {

SARS-CoV-2 virus has caused pandemic disease since the end of 2019. Virus transmission occurs through droplet and infects the host{\textquoteright}s respiratory tract rapidly. Viral propagation occurs through translation process of genome +ssRNA, then it being replicated forming some new body parts of virus and assemblied into virions that ready to infect. During the replication process, the translated viral genome in the form of polyprotein will be cut into smaller components by proteases, which one is 3CLpro. The presence of the 3CLpro receptor is used in drug development through in-silico molecular docking process to minimize failures before laboratory test. The antivirus compounds that used to inhibit the 3CLpro receptor are from gletang plant (Tridax procumbens Linn.). This study aim is to determine the value of binding affinity, the interaction between compounds and receptor, and the effect of drug components. The research was conducted by in-silico through the molecular docking process of 3CLpro receptor and antivirus compounds of gletang (Tridax procumbens Linn.), including betulinic acid, kaempferol and lignan. The results showed that the binding affinity of betulinic acid was -6.6 kcal/mol, kaempferol was -5.6 kcal/ mol and lignan was -5.4 kcal/mol. The interaction form of compounds and receptor was hydrogen bond, electrostatic, hydrophobic, and van der Waals. Compared to baicalein compound as a positive control with the value of binding affinity was -6.7 kcal/mol and its interaction with 3CLpro receptor, showed betulinic acid, kaempferol and lignan have smaller ability but they have the potential to inhibit the 3CLpro receptor.

}, keywords = {3CLpro receptor, Antivirus, Gletang, In-silico, SARS-CoV-2.}, doi = {10.5530/pj.2022.14.170}, author = {Yuna Islamiati and Yani Suryani and Ayuni Adawiyah and Opik Taufiqurrohman and Viol Dhea Kharisma and Devi Purnamasari and Nunuk Hariani Soekamto and Anny Setijo Rahaju and Kuswati and Riso Sari Mandeli and Kawther Ameen Muhammed Saeed Aledresi and Nur Farhana Mohd Yusof and Maksim Rebezov and Shimanovskaya Yanina and Belyakova Natalia and Dmitriy Kulikov and Gulnara Mullagulova and Rahadian Zainul and Muhammad Thoriq Albari} }