HKSA secara In-Silico Senyawa 1-Benzil-3- Benzoilurea dan Analognya sebagai Penghambat Reseptor Bruton Tyrosine Kinase (BTK)

Abstract—In this study, a new anticancer drug design for non-Hodgkin’s lymphoma was carried out, with a molecular docking approach from the compound 1-benzyl-3-benzoylurea parent and its analog as an anticancer compound. The purpose of the study was to obtain the best quantitative structure-activity relationship (QSAR). The in-silico activity test was carried out on the new 1-benzyl-3-benzoilurea and its analog compound against the Bruton Tyrosine Kinase receptor (BTK) PDB code (5FBN) by using the Molegro Virtual Docker 5.5 program and producing a RS (Rerank Score) value for the test compound and Acalabrutinib was used as a comparison. This study also conducted bioavailability by predicting the value of F (intestinal human absorption) in the pkCSM program and toxicity studies by predicting LD50 values using the Protox II program. Correlation and regression were performed using the RS, F, and LD50 values that we obtained on the physicochemical properties of the test compound using the IBM SPSS version 24 program. The best equation is obtained as follows: (1) F = 0.851 Es Taft - 6.116 σ - 1.969 π² + 3.620 π + 90.809; (2) RS = 4.376 Es Taft - 88.802; (3) LD50 = 672.518 CMR - 669.385 ClogP - 813.806. From the results of the best equation is obtained that the activity is influenced by the parameters of steric physicochemical properties (Es Taft). Keywords: 1-benzyl-3-benzoylurea, code pdb:5fbn, in-silico, non-hodgkin lymphoma Abstrak—Pada penelitian ini dilakukan rancangan obat baru antikanker Limfoma non-Hodgkin, dengan pendekatan penambatan molekul dari senyawa induk 1-benzil-3-benzoilurea dan analognya sebagai senyawa antikanker.Tujuan penelitian ini untuk mendapatkan persamaan hubungan struktur aktivitas (HKSA) terbaik. Uji aktivitas in-silico dilakukan terhadap senyawa baru 1-benzil-3-benzoilurea dan analognya terhadap reseptor Bruton Tyrosine Kinase (BTK) kode PDB 5FBN dengan menggunakkan program Molegro Virtual Docker 5.5 dan menghasilkan nilai RS (Rerank Score) untuk senyawa uji dan Acalabrutinib digunakan sebagai pembanding. Penelitian ini juga dilakukan studi bioavaibilitas dengan memprediksi nilai F (intestinal human absorbtion) pada program pkCSM dan studi toksisitas dengan memprediksi nilai LD50 menggunakan program Protox II. Korelasi dan regresi dilakukan menggunakan nilai RS, F dan LD50 yang telah diperoleh terhadap parameter sifat fisikokimia senyawa uji menggunakan program IBM SPSS versi 24. Persamaan terbaik yang diperoleh sebagai berikut: (1) F = - 1.969 π² + 0.851 Es Taft - 6.116 σ + 3.620 π + 90.809 (2) RS = 4.376 Es Taft - 88.802 (3) LD50 = 672.518 CMR - 669.385 ClogP - 813.806. Dari hasil persamaan terbaik tersebut diperoleh bahwa aktivitas dipengaruhi oleh parameter sifat fisikokimia sterik (Es Taft). Kata kunci: 1-benzil-3-benzoilurea, in-silico, kode pdb: 5fbn, limfoma non-hodgkin

Bioinformatic approach of propolis as an inhibitor of peptidoglycan glycosyltransferase to improve antibacterial agent: An in-silico study

Background: In Indonesia, the prevalence of dental and oral problems is still high at 57.6% in 2018, especially periodontitis at 74.1%. Peptidoglycan is an essential component of the bacterial cell wall. Peptidoglycan glycosyltransferase (PGT) is a protein target that plays a role in transferring lipid disaccharides II to growing glycan chains for bacterial cell wall synthesis. Propolis is a natural ingredient produced by bees and has anti-inflammatory, antibacterial, antiviral and antioxidant properties so that it has the potential to be a natural mouthwash ingredient. One of the antibacterial properties of propolis is to be able to kill and reduce the number of bacteria that cause periodontitis. Purpose: This study aims to investigate the potential of a specific compound of propolis as an inhibitor of protein peptidoglycan glycosyltransferase through bonding interactions. Methods: The method used is an in-silico test in molecular docking with computational software, namely Molegro virtual docker and Discovery Studio visualizer. Results: This study showed the types of bonds between the four compounds, and chlorhexidine as a control showed similar types of bonds, including hydrogen bonds, hydrophobic interactions and unfavourable bonds. The binding energy values of each of the five compounds were pinocembrin -222.166 kJ/mol, hesperetin -230.144 kJ/mol, chrysin -219.45 kJ/mol, caffeic acid phenethyl ester -266.64 kJ/mol and chlorhexidine -362.71 kJ/mol. Conclusion: Caffeic acid phenethyl ester (CAPE) is the most significant potential as an inhibitor of protein peptidoglycan glycosyltransferase and chlorhexidine has the highest binding affinity than the four propolis compounds, followed by caffeic acid phenethyl ester in propolis in silico.

As Antimicrobial Agents: Synthesis, Structural Characterization and Molecular Docking study of Barbituric Acid Derivatives from Phenobarbital

In spite of phenobarbital has been used in various medical fields as hypnotics, anxiolytics, and anticonvulsants, it also contains active functional groups that can be reacted to form other products as dyes, polymers, antimicrobial and anti-antioxidants agents. A series of barbituric acid derivatives containing 1,2,3,4-Tetrazoline moiety were synthesized from phenobarbital. Phenobarbital 1 as raw starting material was reacted with acrylonitrile compound to give diacetonitrile derivative 2, this compound was treated in two ways, urea and thiourea to form barbituric acid derivatives containing oxadiazole and thiadiazole ring 3, 4 respectively. The Schiff bases derivatives 5, 6 (a-c) were synthesized from reacting the latter compounds with three aromatic aldehydes. In the final step, the barbituric acid derivatives containing 1,2,3,4Tetrazoline moiety 7, 8 (a-c) were prepared by cycloaddition reaction between different Schiff bases derivatives and sodium azide. The compounds were characterized by Melting point, 13 C-NMR, 1 H-NMR and FTIR techniques. Also, the result compounds were tested against two kinds of bacteria and two kinds of fungi. Most of the prepared derivatives were showed a high and clear effect against different types of bacteria and fungi. Molecular docking of final barbituric acid derivatives 7, 8 (a, b) were investigated with Molegro Virtual Docker (MVD).

Anticancer activity of secondary metabolites from Bauhinia tomentosa Linn. leaf – An in silico approach

Introduction and Aim: Plants and plant derived products are used for human healthcare since the dawn of human civilization. About 80% of modern drugs are from natural origin. Many dreadful diseases like cancer are treated using drugs of natural origin. In the present study, a medicinal plant B. tomentosa Linn. leaves were investigated for its anticancer activity using A549 (Human Adenocarcinomic Alveolar Basal Epithelial Cells) cell lines. The active components were identified using GC-MS (Gas Chromatography- Mass Spectrophotometry) analysis. The aim of the present study was to identify potential lead compounds against various protein targets that are involved in lung carcinogenesis using molecular docking approach. Materials and Methods: 3D structures of compounds reported from GCMS analysis of B. tomentosa were built using Chemsketch software. All the compounds analyzed exhibited antioxidant, anticancer, antimicrobial, anti-inflammatory, and chemo preventive properties. Docking studies were performed using Molegro virtual docker (MVD). Results: The docking studies revealed that the ligands either activate or inhibit the selected target proteins appropriately. This shows that the phytochemicals of B. tomentosa leaf was found to have appreciable anticancer activity. Conclusion: The presence of various bioactive phytoconstituents justifies the use of the leaf for various ailments by traditional practitioners.

The inhibitory Effects of Some Artificial Food Colorings on α-amylase and α-glucosidase: In Vitro and In Silico Studies

Background: Inhibition of α-amylase and α-glucosidase is considered as an important therapeutic target to manage type 2 diabetes mellitus (T2DM), reducing postprandial hyperglycemia (PPHG). Objective: The present work explored the antidiabetic activities of five artificial food colorings by α-amylase and α-glucosidase enzyme inhibition in vitro and in Silico. Methods: In this study, inhibition of α-amylase and α-glucosidase were evaluated. Further, the interaction between enzymes (α-amylase and α-glucosidase) and ligands (food colorings) was followed by QSAR and molecular docking studies. Results: The in vitro results obtained show that the blue patent (SIN131) exhibited more potent inhibition with IC50 values of 0.03± 0.01 mM and 0.014±0.001 mM against α-amylase and α-glucosidase inhibition respectively compared to acarbose. The QSAR study found a strong correlation between IC50 values with four molecular descriptors. This linear regression confirms that a strong polarity (Apol) and a low hydrophobia (ALogP) favor the inhibitory effect of these colorings toward both enzymes. Also, a negative role of the number of heavy atoms has been demonstrated in the phenomenon of inhibition of this enzyme. Finally, the descriptor εlumo (electronic affinity) plays a crucial role on the inhibitory power of these dyes toward both enzymes by electron transfer. The virtual screening of the inhibition of α-amylase and α-glucosidase by these colorings, using Molegro Virtual Docker (MVD), allowed us to obtain stable complexes with interaction energies resulting from the place of hydrogen bonds and several hydrophobic interactions. However, the sulfonate groups of these colorings can be the major factors in the inhibition of these enzymes. On the other hand, Rerank Score with the pose are perfectly correlated (R2> 0.76) to the inhibitory activity of these food colorings measured experimentally. Conclusion: The present study suggests that the Blue Patent V (SIN131) effectively act as α-amylase and α-glucosidase inhibitor leading to a reduction in starch hydrolysis and hence eventually to lowered glucose levels.

New Galantamine Derivatives with Inhibitory Effect on Acetylcholinesterase Activity

Background: Inhibitors of acetylcholinesterase (AChE) are used to treat many disorders, among which are neurodegenerative upsets, like Alzheimer’s disease (AD). One of the limited licensed AChE inhibitors (AChEIs) used as drugs is the natural compound galantamine (Gal). Objective: As Gal is a toxic compound, here we expose data about its four derivatives in hybrid peptide-norgalantamine molecules, which have shown 100 times lower toxicity. Methods: Four newly synthesized galantamine derivatives have been involved in docking analysis made by Molegro Virtual Docker. Biological assessments were performed on ICR male mice. The change in short and long-term memory performance was evaluated by passive avoidance test. AChE activity and levels of main oxidative stress parameters: lipid peroxidation, total glutathione (GSH), enzyme activities of catalase (CAT), superoxide dismutase, and glutathione peroxidase were measured in brain homogenates. Results: Our experimental data revealed that the new hybrid molecules did not impair memory performance in healthy mice. Two of the compounds demonstrated better than Gal AChE inhibitory activity in the brain. None of them changed the level of lipid peroxidation products, one of the compounds increased GSH levels, and all of them increased CAT enzyme activity. Conclusion: The new galantamine-peptide hybrids demonstrated a potential for inhibition of AChE and antioxidant activity and deserve further attention.

Screening and Identification of Potential iNOS Inhibitors to Curtail Cervical Cancer Progression: An in-Silico Drug Repurposing Approach

Cervical cancer is the second most common cause of cancer deaths in women worldwide and remains the main reason of mortality amongst women of reproductive age in developing countries. Nitric oxide is involved in several physiological functions inclusive of inflammatory and immune responses. However, the function of NO in tumor biology is debatable. The inducibleNOS (iNOS/NOS2) isoform is the oneresponsible to maintain the levels of NO and it exhibits pleotropic effects in various cancer with concentration-dependent pro- and anti-tumor effects.NOS2 triggers angiogenesis and endothelial cell migration in tumors by regulating the levels of vascular endothelial growth factor (VEGF). In drug discovery, drug repurposing involves investigations of approved drug candidates to treat various other diseases. In this study, we used FDA-approved anti-cancer drugs and small molecules to target iNOS and identify a potential selective iNOS inhibitor. The structures of ligands were geometrically optimized, and energy minimized using Hyperchem software. Molecular docking was performed using Molegro virtual docker and ligands were selected based on MolDock score,Rerank score, and H-bonding energy. In the study showed 4 compounds, Degarelix, Goserelin, Triptorelin pamoate, and venetoclax demonstrated excellent binding affinity to NOS2 protein. These compounds exhibited the lowest MolDock score, Rerank score, with better H-bonding energy to NOS2. Based on the results theses ligands project to be promising potential NOS2 inhibitors to curtail cervical cancer progression

Pharmacokinetic predictions and docking studies of substituted aryl amine-based triazolopyrimidine designed inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH)

Background The sixteen (16) designed data set of substituted aryl amine-based triazolopyrimidine were docked against Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) employing Molegro Virtual Docker (MVD) software and their pharmacokinetic property determined through SwissADME predictor. Results The docking studies shows compound D16, 5-((6-methoxy-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)amino)benzo[b]thiophen-4-ol to be the most interactive and stable derivative (re-rank score = − 114.205 kcal/mol) resulting from the hydrophobic as well as hydrogen interactions. The hydrogen interaction produced one hydrogen bond with the active residues LEU359 (H∙∙H∙∙O) at a bond distances of 2.2874 Å. All the designed derivatives were found to pass the Lipinski rule of five tests, supporting the drug-likeliness of the designed compounds. Conclusion The ADME analysis revealed a perfect concurrence with the Lipinski Ro5, where the derivatives were found to possess good pharmacokinetic properties such as molar refractivity (MR), number of rotatable bonds (nRotb), log of skin permeability (log Kp), blood-brain barrier (BBB). These results could a deciding factor for the optimization of novel antimalarial compounds.

Phyllanthin and hypophyllanthin, the isolated compounds of Phyllanthus niruri inhibit protein receptor of corona virus (COVID-19) through in silico approach

Objectives Phyllanthus niruri has been known as an immunomodulator and also reported to possess an antiviral activity against several RNA viruses, such as hepatitis B virus and hepatitis C virus by inhibiting viral entry and replication. Since the current situation of Coronavirus Disease 2019 (COVID-19) which infected among the world and caused severe disease and high morbidity, it urgently needed to find new agents against COVID-19. Therefore, in silico screening against COVID-19 receptors is carried out as an initial stage of drug discovery by evaluating the activity of phyllanthin and hypophyllanthin, an isolated from Phyllanthus niruri, in inhibiting spike glycoprotein (6LZG) and main protease (5R7Y) which play as target receptors of COVID-19. Methods Molegro Virtual Docker 6.0 used to determine the best binding energy through the rerank score which shows the total energy bonds calculation. Results Phyllanthin and hypophyllanthin demonstrated to possess greater binding affinity toward the COVID-19 inhibition sites than their native ligand. The rerank score of phyllanthin and hypophyllanthin are lower than the native ligands 6LZG and 5R7Y. This result indicated that phyllanthin and hypophyllanthin have a stronger interaction than the native ligands both in spike glycoprotein (entry inhibitor) and main protease (translation and replication inhibitor). Conclusions In conclusion, phyllanthin and hypophyllanthin are predicted to have strong activity against COVID-19 through inhibiting spike glycoprotein and main protease under in silico study. Further research is needed to support the development of P. niruri as inhibitor agents of COVID-19 through bioassay studies.

Synthesis, characterization, molecular docking and in vitro anticancer activity of 3-(4-methoxyphenyl)-5-substituted phenyl-2-pyrazoline-1- carbothioamide

In the present study, eight numbers of new 3- (4-methoxy phenyl)-5-substituted phenyl-2-pyrazoline-1-carbothioamide (5a-h) have been synthesized from 1- (4-methoxy phenyl)-3- (substituted phenyl)-prop-2-en-1-one (3a-h) and structurally characterized by using FT-IR, 1H NMR, 13C NMR, Mass and Elemental analysis. The synthesized molecules were biologically evaluated for their in vitro anticancer activity against human breast adenocarcinoma (MCF-7), liver cancer (Hep-G2) and leukaemia cancer (K-562) cell line using Sulforhodamine B (SRB) bioassay technique. From the all synthesized compounds 5a, 5c, 5d, and 5e exhibited potent anticancer activity (GI50= <10µg/ml) as compared to the controlled drug 5-Fluorouracil (5-FU) (GI50=44.5µg/ml) and Adriamycin (ADR) (GI50= <10µg/ml) on MCF-7 cell lines. Besides this, all the synthesized compounds have exhibited moderate activity against human liver cancer (Hep-G2) and leukaemia cancer (K-562) cell lines. In addition, molecular docking studies were also explored in order to study the probable binding specificity into the active site of Epidermal Growth Factor Receptor tyrosine kinase (EGFR) (PDB ID: 1M17) using Molegro Virtual Docker Evaluation 2013 6.0.1 (MVD). Based on the molecular docking result, it was found that compound 5a exhibited the best interaction with the above target (i.e., EGFR) by interacting with specific amino acid residues such as: Thr 766, Gin 767, Thr 830, Cys 575, Ala 719 and Met 769.