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All Journal HAYATI Journal of Biosciences Indonesian Journal of Pharmaceutical Science and Technology Indonesian Journal of Biotechnology Health Notions Jurnal Biodjati Al-Kimia Chimica et Natura Acta Jurnal Pendidikan Kimia (JPKim) Indonesian Journal of Chemistry Jurnal Ilmiah Berkala: Sains dan Terapan Kimia Jurnal Sains dan Teknologi Farmasi Indonesia al Kimiya : Jurnal Ilmu Kimia dan Terapan Journal of Tropical Pharmacy and Chemistry Jurnal Sains dan Kesehatan
Muhammad Yusuf
Departemen Kimia, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Universitas Padjadjaran
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Dentistry Earth & Planetary Sciences Education Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Nursing Public Health

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Exploring the Potency of Nigella sativa Seed in Inhibiting SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations Ari Hardianto; Muhammad Yusuf; Ika Wiani Hidayat; Safri Ishmayana; Ukun Mochammad Syukur Soedjanaatmadja
Indonesian Journal of Chemistry Vol 21, No 5 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.65951

Abstract

Coronavirus disease (COVID-19) is a pandemic burdening the global economy. It is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Black cumin (Nigella sativa) seed may contain antivirals for the disease since it was reported to inhibit the human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Main protease (Mpro) is a vital protein for viral replication and a promising target for COVID-19 drug development. Hence, in this study, we intended to uncover the potency of N. sativa seed as the natural source of inhibitors for SARS-CoV-2 Mpro. We collected secondary metabolites in N. sativa seed through a literature search and employed Lipinski’s rule of five as the initial filter. Subsequently, virtual screening campaigns using a molecular docking method were performed, with N3 inhibitor and leupeptin as reference ligands. The top hits were analyzed further using a molecular dynamics simulation approach. Molecular dynamics simulations showed that binding affinities of nigellamine A2 and A3 to Mpro are comparable to that of leupeptin, with median values of -43.9 and -36.2 kcal mol–1, respectively. Ultimately, this study provides scientific information regarding N. sativa seeds’ potency against COVID-19 and helps direct further wet experiments.
An Electrochemical Aptasensor for the Detection of HER2 as a Breast Cancer Biomarker Based on Gold Nanoparticles-Aptamer Bioconjugates Yeni Wahyuni Hartati; Sari Syahruni; Shabarni Gaffar; Santhy Wyantuti; Muhammad Yusuf; Toto Subroto
Indonesian Journal of Chemistry Vol 21, No 6 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.67124

Abstract

Inaccurate diagnoses contributes to the high mortality rate of breast cancer. Human epidermal growth factor receptor 2 (HER2) is overexpressed in breast cancer tumors at around 20–30%. This study aims to develop an electrochemical biosensor for HER2 based on a gold nanoparticle-aptamer bioconjugate (AuNP@HER2 aptamer) and investigate the interaction between DNA aptamer and HER2 using computational methods. The bioconjugate was synthesized using maleimide and polyethylene glycol as a linker. The –NH2 group of cysteamine that modified the gold electrode can form a covalent bond with the bioconjugate maleimide. The interaction of the bioconjugated aptamer with HER2 was measured electrochemically based on the [Fe(CN)6]3−/4− redox system. The limit of detection, the linear range of HER2, precision, and accuracy in this study were 1.52 ng mL–1, 0.01 to 15.0 ng mL–1, 0.1298, and 94.06%, respectively. The structure of the DNA aptamer was modeled using mFold, Assemble2, and Chimera, with the interaction between the DNA aptamer and HER2 explored by NPDock. The modeling of the aptamer with HER2 showed that electrostatic interactions dominated the attractive forces. The resulting interaction pattern can be used as a template to improve the binding energy of the aptamer, thus providing insight into the development of aptamer-based biosensors.
Computational Design of Nanobody Binding to Cortisol to Improve Their Binding Affinity Using Molecular Docking and Molecular Dynamics Simulations Umi Baroroh; Nur Asni Setiani; Irma Mardiah; Dewi Astriany; Muhammad Yusuf
Indonesian Journal of Chemistry Vol 22, No 2 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.71480

Abstract

Currently, nanobody binding cortisol has been deposited in the database. Unfortunately, the affinity is still in micromolar order. Substituting hydrophobic residues in the binding pocket and utilizing CDR2 and CDR3 is the strategy to improve the affinity. A single and double substitution at positions 53 and 101 have been introduced to the nanobody structure through molecular modeling. The affinity toward cortisol was evaluated using molecular docking to get the binding pose. The highest binding energy pose was used as the initial coordinate to analyze further using 100 ns molecular dynamics simulations. The binding affinities calculated by MMGBSA showed that MT3, MT5, and MT6 have better binding affinity than WT. In contrast, the ligand movement through MD simulations reveals that MT1, MT3, and MT5 are relatively stable. Hence, docking and MD simulations showed that MT3 is the best mutant than others. This mutant is substituting the threonine to isoleucine at position 53. New hydrophobic interactions occurred and caused the increase of binding. Eventually, this study provides valuable structural information to improve the binding affinity of nanobody binding cortisol for further development of this molecule to antibody-based biosensor design. 
PERBANDINGAN METODE SINTESIS DAN KARAKTERISASI ETILENDIAMIN-FOLAT SEBAGAI PREKURSOR PEMBUATAN SENYAWA PENGONTRAS MRI GADOLINIUM DIETILENTRIAMINPENTAASETAT-FOLAT Retna Putri Fauzia; Abdul Mutalib; R Ukun M S Soedjanaatmadja; Anni Anggraeni; Zuhrotun Nafisah; Muhammad Yusuf; Husein H Bahti
Jurnal Sains dan Terapan Kimia Vol 11, No 1 (2017)
Publisher : Program Studi Kimia, Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (560.162 KB) | DOI: 10.20527/jstk.v11i1.3168

Abstract

Early development of self‐administered COVID‐19 rapid test based on nucleocapsid detection in saliva sample Siti Soidah; Toto Subroto; Sari Syahruni; Fauzian Giansyah; Henry Chandra; Dhiya Salsabila; Bachti Alisjahbana; Nisa Fauziah; Hesti Lina Wiraswati; Leonardus Wiydatmoko; Basti Andriyoko; Anita Yuwita; Muhammad Yusuf
Indonesian Journal of Biotechnology Vol 27, No 3 (2022)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.72269

Abstract

More than 6,000,000 people have died due to the coronavirus (COVID‐19) pandemic. This disease spread quickly due to its highly contagious nature. The SARS‐CoV‐2 virus that causes the disease can be transmitted through saliva droplets secreted by infected people at a distance of less than 1 m. As a result, saliva has been accepted as an alternative specimen for COVID‐19 detection by the Centers for Disease Control and Prevention (CDC). Furthermore, WHO recommended the use of rapid antigen tests based on lateral flow immunoassay when reverse transcription‐polymerase chain reaction (RT‐PCR) is not available. We developed a saliva‐based rapid antigen test by optimizing the antibody concentration and optimum pH for the conjugation of antibody and gold nanoparticles. We found that the best running buffer formulation consisted of 75 mM sodium phosphate buffer, 1% NaCl, 1% Triton X‐100, 0.5% N‐acetyl‐L‐cysteine, and 0.02% sodium azide. The addition of a mucolytic agent in the buffer can reduce the viscosity of saliva, thus improving sensitivity. The rapid test developed detected the lowest concentration of nucleocapsid protein at 0.1 μg/mL. Our study revealed 100% specificity against negative COVID‐19 saliva and no cross‐reaction with avian influenza virus hemagglutinin.
The Stability Study of Electrochemical Aptasensor to Detect SARS-CoV-2 Spike Protein and Its Application for Clinical Samples of Nasopharyngeal Swab Arum Kurnia Sari; Ghina Nur Fadhilah; Irkham Irkham; Muhammad Yusuf; Shabarni Gaffar; Yeni Wahyuni Hartati
Indonesian Journal of Chemistry Vol 23, No 2 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.77887

Abstract

The stability characteristics associated with the shelf life of a biosensor are rarely investigated, however, they are important factors for real applications. Stability is the variation in the detection signal over a long period of storage. This study aims to determine the effect of storage time on the stability of SARS-CoV-2 receptor binding domain (RBD) spike protein aptamers related to shelf life and the performance of an electrochemical aptasensor on clinical samples. The research method includes a stability study conducted using the accelerated stability method based on the Arrhenius equation at three variations of temperature and storage time. The electrochemical aptasensor's performance was evaluated on clinical samples of 32 nasopharyngeal swabs at biosafety level 3 and its potential on clinical saliva samples. The results indicated that the developed electrochemical aptasensor was stable for ± 15 days with a shelf life of 18, 17 and 16 days, respectively, at 25, 40 and 50 °C. This electrochemical aptasensor has the potential to be a Point of Care (POC) device for the clinical detection of SARS-CoV-2 because it can be tested on clinical samples of nasopharyngeal swabs and the results show its potential application to detect in clinical saliva samples.
A Computational Study of Fab CHK152 with CHK265 as Anti Chikungunya Virus for Rapid Test Components Korry Novitriani; Ade Rizki Ridwan Firdaus; Bacthi Alisjahbana; Shabarni Gaffar; Muhammad Yusuf; Toto Subroto
Health Notions Vol 7, No 5 (2023): May
Publisher : Humanistic Network for Science and Technology (HNST)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33846/hn70502

Abstract

The symptoms of chikungunya disease are generally similar to the symptoms of other viral diseases, except that chikungunya disease can cause joint disorders and even paralysis. Incorrect initial diagnosis will result in inappropriate treatment of the disease Thus it is necessary to study the identified antibodies that can neutralize and protect the body from alphavirus infections, including chikungunya. There are several antibodies that can neutralize chikungunya including CHK152 which neutralizes virus by inhibiting fusion with stabilizing the surface area of the virus, hindering the exposure of the fusion-loop, likely neutralizing infection by blocking fusion. Otherwise CHK265 inhibits the life cycle of the virus in a way neutralize infection by blocking entry at a post-attachment pre-fusion step. The low energy of binding between antigen-antibodies will stabilize the interaction of both. Therefore, this aims to find the best affinity energy for antibodies to be used in the rapid diagnostic component of anti-chikungunya virus (CHIKV). The binding energies were calculated using FireDock an efficient method for the refinement and rescoring of rigid-body docking solutions, through rearrangement of the interface sidechains and adjustment of the relative orientation of the molecules.The results of this study  obtained energy scores from CKH152 and CHK265 are -125.78 and -29.94, indicate that CHK265 antibody affinity energy is higher than CHK152. It can be concluded that the best affinity energy for CHIKV diagnostic component is CHK152.Keywords: energy affinity; CHK152; CHK265; E1E2 CHIKV; molecular docking
Study on the Mitochondrial Genome of Variants Carrying mt.3243A>G from Type-2 Diabetes Mellitus and Cataract Patients in Indonesia Iman Permana Maksum; Rahmaniar Mulyani; Khomairi Hasan; Mamlikatu Ilmi Azizah; Wanda Destiarani; Ahmad Fariz Maulana; Muhammad Yusuf; Toto Subroto
HAYATI Journal of Biosciences Vol. 30 No. 6 (2023): November 2023
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.30.6.1017-1024

Abstract

The association of type-2 diabetes mellitus (T2DM) and cataract with mtDNA mutation has been reported before. Despite the high prevalence of DM and cataract in Indonesia, a study of the mtDNA variants in Indonesia in correlation with the two diseases is still limited. MT.3243A>G is one of the hotspots mutations for mitochondrial diseases, but the explanation for its occurrence in patients with pure cataract is still elusive. Therefore, the objective of this study was to analyze the mitochondrial genome variants from T2DM and cataract patients in Indonesia using the direct sequencing method. The homology analysis of the genome to the Cambridge reference sequence resulted in 86 variants, including 20 variants that cause amino acid substitutions. Based on the Mitomap data, 17 of the 20 variants were novel. Upon comparison with the 12 normal variant genomes, 11 of 17 variants were suggested to be associated with T2DM and cataract diseases since they code the protein in complex-I (ND4L, ND5, and ND6), complex-III (cytb), and complex-V (ATP6) of the respiratory complex. Interestingly, MT.3316G>A, for the first time, is shown in a pure cataract patient. In addition, the novel phenotype of MT.5460G>A and MT.10398A>G were revealed, which are T2DM and cataract in one patient. Based on our study, these diseases might be related to the disruption of the ATP metabolism due to the structure and function changes of proteins involved in the respiratory complex. This discovery is expected to offer an understanding of the origins of gene-level clinical differences, particularly in Indonesia.
Comparative assessment of human salivary α-amylase inhibitor from Indonesian herbs Khomaini Hasan; Angga Himas Setyawan; Muhamad Abidin; Nurul Aida Fathya; Dewi Ratih Handayani; Desy Linasari; Saronom Silaban; Toto Subroto; Muhammad Yusuf
Jurnal Pendidikan Kimia (JPKIM) Vol 15, No 3 (2023): December
Publisher : Pascasarjana Universitas Negeri Medan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24114/jpkim.v15i3.51153

Abstract

Diabetes mellitus (DM) is a multifactorial disease defined by persistent hyperglycemia and impaired carbohydrate, lipid, and protein metabolism due to a lack of insulin secretion. The objective of this study was to assess the Indonesian herbs which have the ability to act as human salivary α-amylase inhibitors, thus, that they can be implemented for medical purposes. In this study, fifteen Indonesian herbs were assessed for their capability as α-amylase inhibitor. The water-reflux method was used to extract all potential water-soluble active components. The Fuwa technique was used to test α-amylase activity. There were significant variations in the effects of herbs on salivary α-amylase activity, according to the statistical using one-way ANOVA and Post Hoc Tukey between the with and without inhibitors. According to the findings, Turmeric (Curcuma longa L.) and pandan leaf (Pandanus amaryllifolius Roxb) had the highest inhibitory power (80%).Keywords: Diabetes mellitus; Flavonoids; Herbs; α-amylase inhibitors
Protein Modelling Insight to the Poor Sensitivity of Chikungunya Diagnostics on Indonesia’s Chikungunya Virus Bevi Lidya; Muhammad Yusuf; Umi Baroroh; Korry Novitriani; Bachti Alisjahbana; Iman Rahayu; Toto Subroto
Indonesian Journal of Chemistry Vol 23, No 5 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.79301

Abstract

Sensitive detection of infectious diseases is crucial for effective clinical care. However, commercial rapid tests may be limited in their ability to detect pathogen variants across different countries. It was found that the sensitivity of a chikungunya rapid test on local strain was only 20.5% as compared to the East, Central, and South Africa (ECSA) phylogroup. Therefore, the development of geographically specific diagnostics is essential. Investigating the distinctive structural properties of a locally sourced antigenic protein is an important initiative for the development of a specific antibody. This study utilized structural bioinformatics and molecular dynamics simulations to investigate the differences between the E1-E2 antigenic proteins of the Indonesian chikungunya virus (Ind-CHIKV) and that of ECSA. The results showed that some of the mutation points are located at the antibody binding sites of Ind-CHIKV. G194S and V318R mutations were proposed as distinctive features of Ind-CHIKV, leading to weaker antibody binding compared to ECSA. It suggests that modifying the antibody to accommodate bulkier side chains at positions 194 and 318 could improve its effectiveness against Ind-CHIKV. These insights are valuable for developing a highly sensitive immunoassay for Ind-CHIKV and other regional pathogens, ultimately enhancing diagnostic capabilities in Indonesia.
Co-Authors Abdul Mutalib Abdul Mutalib Abdul Mutalib Abdul Mutholib Ade Rizki Ridwan Firdaus Ade Rizqi Ridwan Firdaus Agus Safari Agus Safari Agus Safari Ahmad Fariz Maulana Ahsanul Chaliqin Gayo Anceu Murniati Angga Himas Setyawan Anita Yuwita Anneke Noviyanti Anni Anggraeni Anni Anggraeni Anni Anggraeni Annisyaban Fatiha Azzahra Ari Hardianto Arum Kurnia Sari Ashary Fathul Hafidh Bachti Alisjahbana Bacthi Alisjahbana Baroroh, Umi Basti Andriyoko Bayu Shiddiq Widhi Pratama Bevi Lidya Clara Claudia Desy Linasari Dewi Astriany Dewi Astriany Dewi Ratih Handayani Dhiya Salsabila Elsa Destiana Endah Wulandari Farhan Azhwin Maulana Fauzian Giansyah Fauziyah, Hanifa Ghina Nur Fadhilah Henry Chandra Herman Herman Hesein H. Bahti Hesti Lina Wiraswati Husein Hernadi Bahti Idar Idar Idar Idar Ika Wiani Imam Adi Wicaksono Iman Permana Maksum Iman Rahayu Irkham Irkham Irma Mardiah Khomaini Hasan Khomairi Hasan Korry Novitriani Korry Novitriani, Korry Leonardus Wiydatmoko Mamlikatu Ilmi Azizah Martalena Ramli Mia Tria Novianti Mia Widyaningsih Muchtaridi Muchtaridi Muhamad Abidin Muhamad Abidin Muhammad Fadhlillah Nisa Fauziah Novianti, Mia Tria Nur Asni Setiani Nurul Aida Fathya Opik Taupiqurrohman R. Ukun M.S. Soedjanaatmadja Rahmaniar Mulyani Ratna Sari Dewi Ratna Sari Dewi Regaputra Satria Janitra Retna Putri Fauzia Rima Handiyani Rina Fajri Nuwarda Rista Awalia Rudi Hartono Saadah D. Rachman Saadah D. Rachman Saadah Diana Rachman Safri Ishmayana Safri Ishmayana Safri Ishmayana Safri Ishmayana Safri Ishmayana Santhy Wyantuti Sari Syahruni Sari Syahruni Saronom Silaban Shabarni Gaffar Shabarni Gaffar Shabarni Gaffar Shabarni Gaffar Shabarni Gaffar Shinta Kusumawardani Shinta Kusumawardani Siti Soidah Soni Muhsinin Sukma Nuswantara Sylvi Qurrotul Aini Taufik Ramdani Tohari Toto Subroto Toto Subroto Toto Subroto Toto Subroto Toto Subroto Umi Baroroh Umi Baroroh Wahyu Widayat Wanda Destiarani Yani Suryani Yeni Wahyuni Hartati Yeni Wahyuni Hartati Yurika Sastyarina Yurika Sastyarina Zelika Mega Ramadhania Zuhrotun Nafisah Zuhrotun Nafisah