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All Journal Indonesian Journal of Chemistry Journal of Multidisciplinary Applied Natural Science Makara Journal of Science Molekul: Jurnal Ilmiah Kimia
Prasetyo, Niko
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Physics

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The Explosive Sensitivity on the Complex Formation of 3-Nitro-1,2,4-Triazol-5-One and Metal Ions Based on Density Functional Study Hadisaputra, Saprizal; Prasetyo, Niko
Makara Journal of Science Vol. 20, No. 2
Publisher : UI Scholars Hub

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

Abstract

The explosive sensitivity upon the formation of supramolecular interaction between the nitro group of 3-nitro-1,2,4-triazol-5-one (NTO) and metal ions (Mn+ = Li+, Na+, Be2+ and Mg2+) has been investigated using Density Functional Theory at B3LYP/6-311++G** level of theory. The bond dissociation energy (BDE) of the C1–N6 trigger bond has also been discussed for the NTO monomer and the corresponding complexes. The interaction and bond dissociation energy of the C6–N7 trigger bond follow the order of NTO-Be2+ > NTO-Mg2+ > NTO-Li+ > NTO-Na+ > NTO monomer. The enhancement of the trigger bond dissociation energy in comparison with the NTO monomer correlates well with the complex interaction energies, trigger bond length, and charge transfer. The analyses of electron density shifts have shown that the electron density of the nitro group shifts toward the C1–N6 trigger bond upon the formation of the supramolecular interaction. As result, the trigger bond is strengthened and the sensitivity of NTO is reduced. Some of the calculated results agree with the experimental values.
Exploring The Inhibition of SARS-COV-2 PLpro: Docking and Molecular Dynamics Simulation of Flavonoid in Red Fruit Papua and Its Derivatives Ananto, Agus Dwi; Pranowo, Harno Dwi; Haryadi, Winarto; Prasetyo, Niko
Molekul Vol 19 No 3 (2024)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2024.19.3.11717

Abstract

In early 2024, Covid-19 witnessed a substantial decline in cases. Nevertheless, with lingering cases and fatalities persisting, it remains crucial to focus on research to develop patented medicines to inhibit the spread of this virus effectively. This study focuses on the Papain-like protease (PLpro) of SARS-CoV-2 because of its crucial role in the viral life cycle, where it is vital for processing precursor proteins into functional components required for viral replication and propagation. This study investigated the inhibitory potential of flavonoid compounds derived from red fruit (Pandanus conoideus Lam) and their derivatives against SARS-CoV-2 PLpro. Employing an in silico approach through molecular docking and MD simulation, internal validation was conducted by redocking the native ligand 100 times, resulting in an average RMSD of 0.228. The Molecular Docking stage conducted for all flavonoid compounds found in red fruit revealed that Quercetin 3′-glucoside exhibited a binding energy of -8.2440 Kcal/mol, surpassing its comparators, remdesivir and paxlovid, which recorded binding energies of -8.2590 Kcal/mol and -7.2170 Kcal/mol, respectively. Consequently, Quercetin 3′-glucoside was selected as a reference compound for identifying derivative compounds. Subsequently, a derivative compound coded DN5 (2-hydroxy-5-(3,5,7-trihydroxy-4-oxo-4H-chromen-2-yl)phenyl 2-methoxybenzoate) was obtained, demonstrating a higher binding energy than the reference compound, remdesivir, and paxlovid, with a value of -8.9300 Kcal/mol. Molecular dynamic simulations over 100 ns at 300 K further validated the stability of DN5's structure, supported by the presence of hydrogen bonds, van der Waals bonds, and several other bonds, underscoring its potential to inhibit SARS-CoV-2 PLpro and positioning it as a promising candidate for drug development. Keywords: Docking, MD Simulation, red fruit, SARS-CoV-2 PLpro
Investigation of New 4-Benzyloxy-2-trichloromethylquinazoline Derivatives as Plasmodium falciparum Dihydrofolate Reductase-thymidylate Synthase Inhibitors: QSAR, ADME, Drug-likeness, Toxicity, Molecular Docking and Molecular Dynamics Simulation Yogaswara, Radite; Pranowo, Harno Dwi; Prasetyo, Niko; Pulung, Maria Ludya
Journal of Multidisciplinary Applied Natural Science Vol. 5 No. 2 (2025): Journal of Multidisciplinary Applied Natural Science
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.258

Abstract

Plasmonium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) is one of the most crucial antimalarial targets. Mutations in the binding pocket of this target lead to resistance to the antifolate. The mutations influence the amino acid residues at points 51, 59, 108 and 164 and contribute significantly to malaria not being treated well. Priority should therefore be given to the development of antifolate-resistance drugs. These studies aim to investigate new 4-benzyloxy-2-trichloromethylquinazoline derivatives as PfDHFR-TS inhibitors using QSAR, ADME, drug-likeness, toxicity, molecular docking studies, and molecular dynamics simulations. The best equation model from the QSAR analysis used MLR and PLS statistics to show that the pIC50 is linearly related to GATS4e, SpMax AEA(ed), and Mor28e, but inverted when compared to ATS6m and ATSC7m. The predictive ability of the model was confirmed by internal and external validation. In addition, the Y-randomization validation showed that the QSAR model was reliable, robust, and stable, with a cRp2 score of over 0.5. ADME and drug-likeness predictions confirmed the new QSAR design for molecules S10, S23 and S64. Based on the toxicity results, three molecules are expected to have moderate and non-toxic properties, starting with S23 and then S10 and S64. Molecular docking studies show that all three molecules have high binding energies, 9.869, 9.589, and 9.565 kcal/mol. The amino acid residues Leu46, Asp54, Ser111, and Thr185 play a major role in ligand-receptor interaction in the binding pocket of quadruple mutant PfDHFR-TS. Furthermore, an evaluation of molecular dynamics simulations of three complexes S10-3JSU, S23-3JSU and S64-3JSU demonstrated stable interactions over 100 ns.
Unlocking the Potential of Papuan Red Fruit (Pandanus conoideus Lamk): A Comprehensive Exploration of Its Role in COVID-19 Inhibition Through Molecular Docking and Molecular Dynamics Simulation Ananto, Agus Dwi; Pranowo, Harno Dwi; Haryadi, Winarto; Prasetyo, Niko
Indonesian Journal of Chemistry Vol 25, No 3 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.99486

Abstract

Indonesia's rich flora has long been used in traditional herbal medicine, and scientific research is now confirming the health benefits of these plants. Among them, Papuan Red Fruit is gaining attention for its potential in treating various ailments, including COVID-19, due to its antioxidant and antibacterial properties. This study focuses on using in silico methods to investigate how Papuan Red Fruit might inhibit COVID-19, specifically by targeting the papain-like protease (PLpro), a key protein in viral replication. Molecular docking and molecular dynamics (MD) simulations were used to assess the binding affinity and stability of compounds from the fruit. The compound quercetin 3'-glucoside showed the lowest binding energy, indicating strong interactions with PLpro. MD simulations at 300 K for 100 ns confirmed the stability of the quercetin 3'-glucoside-PLpro complex, revealing hydrogen bonds with residues like GLN169. The simulations showed an average delta RMSD of 0.2702 Å, indicating the complex's stability. Overall, this research highlights the potential of Papuan Red Fruit as a natural treatment for COVID-19, opening the door for further studies in drug development.
Co-Authors Agus Dwi Ananto, Agus Harno Dwi Pranowo Pulung, Maria Ludya Saprizal Hadisaputra Winarto Haryadi Yogaswara, Radite