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All Journal Jurnal Masyarakat Informatika Indonesian Journal of Chemistry Journal of Multidisciplinary Applied Natural Science
Faris Hermawan, Faris
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Physics

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Design of Hydroxyxanthone Derivatives as Breast Cancer Inhibitors: A QSAR Modeling, Molecular Docking, Molecular Dynamics, MM-PBSA and ADMET Prediction Fatmasari, Nela; Hermawan, Faris; Jumina, Jumina; Kurniawan, Yehezkiel Steven; Pranowo, Harno Dwi; Puspitasari, Anita Dwi; Hastuti, Lathifah Puji; Marlina, Lala Adetia; Putra, Nicky Rahmana
Journal of Multidisciplinary Applied Natural Science Articles in Press
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.283

Abstract

A comprehensive QSAR analysis, in conjunction with molecular docking, molecular dynamics simulations, MM-PBSA binding energy estimations, and ADMET profiling, was conducted to facilitate the development of novel anticancer agents based on hydroxyxanthone derivatives. Molecular and electronic descriptors were calculated using the DFT method with the 3-21G basis set. The best QSAR model identified several descriptors that significantly influence anticancer activity, including the atomic charges at positions C1, C3, C4a, and C7, as well as the highest occupied molecular orbital (HOMO), surface area (SA), molecular volume (VOL), and molecular weight (MW). This model was used to design novel hydroxyxanthone derivatives (X27 to X47). The docking result showed that compounds 7-bromo-3-hydroxy-1-(methylamino)-9H-xanthen-9-one (X43), 6-hydroxy-8-(methylamino)-9-oxo-9H-xanthene-2-carbonitrile (X44), and 3-hydroxy-7-mercapto-1-(methylamino)-9H-xanthen-9-one (X45) had stronger binding energy values than gefitinib as a native ligand. Gefitinib had a binding energy of -6.84 kcal/mol, while those compounds had values of -6.92, -7.12, and -6.92 kcal/mol, respectively. In a molecular dynamics simulation of 100 ns, compounds X43, X44, and X45 exhibited stability comparable to that of gefitinib against the EGFR protein. Additionally, the binding energy MM-PBSA of compound X43 was the lowest (-29.18 kcal/mol), followed by X44 (-27.11 kcal/mol), gefitinib (-26.06 kcal/mol), and X45 (-25.21 kcal/mol). Furthermore, these compounds met Lipinski's rule parameters and the minimal standard parameters in terms of ADMET characteristics, as predicted by physicochemical properties. In conclusion, compounds X43, X44, and X45 are potential anticancer agents for MDA-MB-231 breast cancer cells.
Artificial Intelligence-Aided In Silico Screening of Syzygium polyanthum Phytochemicals for Antidiabetic Drug Discovery Using ACO (Ant Colony Optimization) Algorithm Samsuri, Ahmad; Hermawan, Faris; Zikri, Adi Tiara; Vifta, Rissa Laila; Puspitasari, Anita Dwi
Jurnal Masyarakat Informatika Vol 16, No 2 (2025): Issue in Progress
Publisher : Department of Informatics, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jmasif.16.2.73574

Abstract

This research employs an artificial intelligence (AI)-driven molecular docking approach to identify potential antidiabetic compounds from Syzygium polyanthum phytochemicals targeting the α-glucosidase enzyme. The docking simulations were conducted using the PLANTS software, which utilizes an ant colony optimization (ACO) algorithm, a nature-inspired AI technique that mimics the foraging behavior of ants to explore ligand binding conformations efficiently. PLANTS integrates multiple empirical scoring functions, including ChemPLP, to evaluate protein-ligand interactions by modeling steric complementarity, hydrogen bonding, and torsional potentials, enabling accurate prediction of binding affinities. The protein structure with PDB code 2JKE was validated with a root-mean-square deviation (RMSD) of 0.2912 Å, confirming the reliability of the docking protocol. Screening results revealed seven phytochemical compounds Hexadecanoic acid 2-hydroxy-1-(hydroxymethyl), Methyl oleate, Methyl palmitate, Phytol, 9,12,15-Octadecatrien-1-ol, Nerolidol, and Eicosane exhibited lower docking scores (-96.2919 to -80.5188) than both the reference drug miglitol (-80.2642) and the native ligand (-77.2910), indicating stronger and more stable binding to the α-glucosidase active site. These findings suggest that the identified compounds have superior theoretical inhibitory potential compared to miglitol, a clinically used α-glucosidase inhibitor. The AI-based in silico screening using PLANTS thus provides a powerful, cost-effective strategy for accelerating antidiabetic drug discovery by prioritizing promising natural compounds for further experimental validation.
Free Radical Scavenging Activity of Chlorochalcones: An Integrated Computational and Experimental Study Puspitasari, Anita Dwi; Ulfah, Maria; Hartati, Indah; Vifta, Rissa Laila; Hermawan, Faris; Ekasari, Munifilia; Marlina, Lala Adetia
Indonesian Journal of Chemistry Vol 25, No 5 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.106221

Abstract

Chlorochalcone derivatives (chalcones 1–3) were synthesized using ultrasound-assisted Claisen-Schmidt condensation, yielding > 80%. Antioxidant activity was evaluated through DPPH and ABTS assays, demonstrating strong activity with IC50 values ranging from 61.52 ± 0.97 to 98.27 ± 1.42 ppm. Chalcones 1 and 2 show SPF potential at 40 ppm and chalcone 3 at 20 ppm (SPF 19.47 ± 0.46). ADMET analysis using the pkCSM tool confirmed favorable pharmacokinetic profiles and low toxicity, supporting their safety for potential applications. Additionally, density functional theory calculations provided more profound insights into molecular stability and reactivity, including electronic properties such as HOMO-LUMO gaps, further corroborating their pharmacological efficacy. These results collectively indicate that chalcones 1–3 exhibit potent antioxidant activity, adequate UV protection, and promising pharmacokinetic properties. Integrating in vitro, in silico, and DFT analyses underscores their potential as multifunctional compounds for antioxidant and sunscreen applications.
Co-Authors Anita Dwi Puspitasari Fatmasari, Nela Harno Dwi Pranowo Indah Hartati Jumina Jumina Kurniawan, Yehezkiel Steven Lathifah Puji Hastuti Maria Ulfah Marlina, Lala Adetia Munifilia Ekasari Putra, Nicky Rahmana Samsuri, Ahmad vifta, rissa laila Zikri, Adi Tiara