1
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Milusheva M, Stoyanova M, Gledacheva V, Stefanova I, Todorova M, Pencheva M, Stojnova K, Tsoneva S, Nedialkov P, Nikolova S. 2-Amino- N-Phenethylbenzamides for Irritable Bowel Syndrome Treatment. Molecules 2024; 29:3375. [PMID: 39064953 PMCID: PMC11280360 DOI: 10.3390/molecules29143375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Irritable bowel syndrome (IBS) is a common gastrointestinal (GI) disorder characterized by abdominal pain or discomfort. Mebeverine is an antispasmodic that has been widely used in clinical practice to relieve the symptoms of IBS. However, its systemic use usually leads to side effects. Therefore, the current paper aimed to synthesize more effective medicines for IBS treatment. We used ring opening of isatoic anhydride for the synthesis in reaction with 2-phenylethylamine. In silico simulation predicted spasmolytic activity for 2-amino-N-phenethylbenzamides. The newly synthesized compounds demonstrated a relaxation effect similar to mebeverine but did not affect the serotonin or Ca2+-dependent signaling pathway of contractile activity (CA) in contrast. Having in mind the anti-inflammatory potential of antispasmodics, the synthesized molecules were tested in vitro and ex vivo for their anti-inflammatory effects. Four of the newly synthesized compounds demonstrated very good activity by preventing albumin denaturation compared to anti-inflammatory drugs/agents well-established in medicinal practice. The newly synthesized compounds also inhibited the expression of interleukin-1β and stimulated the expression of neuronal nitric oxide synthase (nNOS), and, consequently, nitric oxide (NO) synthesis by neurons of the myenteric plexus. This characterizes the newly synthesized compounds as biologically active relaxants, offering a cleaner and more precise application in pharmacological practice, thereby enhancing their potential therapeutic value.
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Affiliation(s)
- Miglena Milusheva
- Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria or (M.M.); (M.S.); (M.T.)
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
| | - Mihaela Stoyanova
- Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria or (M.M.); (M.S.); (M.T.)
| | - Vera Gledacheva
- Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (V.G.); (I.S.); (M.P.)
| | - Iliyana Stefanova
- Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (V.G.); (I.S.); (M.P.)
| | - Mina Todorova
- Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria or (M.M.); (M.S.); (M.T.)
| | - Mina Pencheva
- Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (V.G.); (I.S.); (M.P.)
| | - Kirila Stojnova
- Department of General and Inorganic Chemistry with Methodology of Chemistry Education, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Slava Tsoneva
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria;
| | - Paraskev Nedialkov
- Department of Pharmacognosy, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria;
| | - Stoyanka Nikolova
- Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria or (M.M.); (M.S.); (M.T.)
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2
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Milusheva M, Stoyanova M, Gledacheva V, Stefanova I, Todorova M, Nikolova S. Spasmolytic Activity of 1,3-Disubstituted 3,4-Dihydroisoquinolines. Biomedicines 2024; 12:1556. [PMID: 39062129 PMCID: PMC11275145 DOI: 10.3390/biomedicines12071556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
This article concerns the spasmolytic activities of some novel 1,3-disubstituted 3,4-dihydroisoquinolines. These compounds can be evaluated as potential therapeutic candidates according to Lipinski's rule of five, showing high gastrointestinal absorption and the ability to cross the blood-brain barrier, which is a very important parameter in the drug discovery processes. In silico simulation predicted smooth muscle relaxant activity for all the compounds. Since smooth muscle contractile failure is a characteristic feature of many disorders, in the current paper, we concentrate on the parameters of the spontaneous contractile responses of smooth muscle (SM) cells compared to the well-known drug mebeverine. Two of the newly synthesized substances can be identified as essential modulating regulators and potentially used as therapeutic molecules. One of these molecules also showed significant DPPH antioxidant activity compared to rutin.
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Affiliation(s)
- Miglena Milusheva
- Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria (M.S.); (M.T.)
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria
| | - Mihaela Stoyanova
- Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria (M.S.); (M.T.)
| | - Vera Gledacheva
- Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (V.G.); (I.S.)
| | - Iliyana Stefanova
- Department of Medical Physics and Biophysics, Faculty of Pharmacy, Medical University of Plovdiv, 4002 Plovdiv, Bulgaria; (V.G.); (I.S.)
| | - Mina Todorova
- Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria (M.S.); (M.T.)
| | - Stoyanka Nikolova
- Department of Organic Chemistry, Faculty of Chemistry, University of Plovdiv, 4000 Plovdiv, Bulgaria (M.S.); (M.T.)
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3
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Poleboyina PK, Naik U, Pasha A, Ravinder D, Bhanothu S, Poleboyina SM, Amineni U, Pawar SC. Virtual Screening, Molecular Docking, and Dynamic Simulations Revealed TGF-β1 Potential Inhibitors to Curtail Cervical Cancer Progression. Appl Biochem Biotechnol 2024; 196:1316-1349. [PMID: 37392324 DOI: 10.1007/s12010-023-04608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2023] [Indexed: 07/03/2023]
Abstract
Cervical cancer is one of the main causes of cancer death in women globally, and its epidemiology is similar to that of a low-infectious venereal illness. Many sexual partners and early age at first intercourse have been demonstrated to have a significant influence on risk. TGF-β1 is a multifunctional cytokine that is required for cervical carcinoma metastasis, tumor development, progression, and invasion. The TGF-β1 signaling system plays a paradoxical function in cancer formation, suppressing early-stage tumor growth while increasing tumor progression and metastasis. Importantly, TGF-β1 and TGF-β receptor 1 (TGF-βR1), two components of the TGF-β signaling system, are substantially expressed in a range of cancers, including breast cancer, colon cancer, gastric cancer, and hepatocellular carcinoma. The current study aims to investigate possible inhibitors targeting TGF-β1 using molecular docking and dynamic simulations. To target TGF-β1, we used anti-cancer drugs and small molecules. MVD was utilized for virtual screening, and the highest scoring compound was then subjected to MD simulations using Schrodinger software package v2017-1 (Maestro v11.1) to identify the most favorable lead interactions against TGF-β1. The Nilotinib compound has shown the least XP Gscore of -2.581 kcal/mol, 30ns MD simulations revealing that the Nilotinib- TGF-β1 complex possesses the lowest energy of -77784.917 kcal/mol. Multiple parameters, including Root Mean Square Deviation, Root Mean Square Fluctuation, and Intermolecular Interactions, were used to analyze the simulation trajectory. Based on the results; we conclude that the ligand nilotinib appears to be a promising prospective TGF-β1inhibitor for reducing TGF-β1 expression ad halting cervical cancer progression.
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Affiliation(s)
- Pavan Kumar Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Umakanth Naik
- Department of Bioinformatics, SVIMS University, Tirupati, Andhra Pradesh, 517 507, India
| | - Akbar Pasha
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Doneti Ravinder
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Shivaji Bhanothu
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Sneha Malleswari Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Umamaheshwari Amineni
- Department of Bioinformatics, SVIMS University, Tirupati, Andhra Pradesh, 517 507, India
| | - Smita C Pawar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India.
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4
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Agarwal V, Haldhar R, Hirad AH, Ahmed B, Han SB, Gupta A, Raj V, Lee S. Repurposing FDA-approved drugs as NLRP3 inhibitors against inflammatory diseases: machine learning and molecular simulation approaches. J Biomol Struct Dyn 2024:1-13. [PMID: 38400742 DOI: 10.1080/07391102.2024.2308072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/10/2024] [Indexed: 02/26/2024]
Abstract
Activation of NLRP3 (NOD-like receptor family, pyrin domain-containing protein 3) has been associated with multiple chronic pathologies, including diabetes, atherosclerosis, and rheumatoid arthritis. Moreover, histone deacetylases (HDACs), specifically HDAC6 is required for the NLRP3 inflammasome to assemble and activate. Thus, NLRP3 serves as an attractive target for the development of novel therapeutic approaches. Several companies are now attempting to develop specific modulators of the NLRP3 inflammasome, but only a handful of small molecules of NLRP3 inflammasome inhibitors, such as MCC950 and Tranilast, are currently available for clinical use. However, their use is limited due to severe side effects and short half-lives. Thus, the repurposing of FDA-approved drugs with NLRP3 inhibitory activity is needed. The present study was aimed at repurposing preexisting drugs that might act as safe and effective NLRP3 inhibitors. A library of 2,697 FDA-approved drugs was screened for binding with NLRP3 (PDB: 7ALV) using Glide (Schrödinger). The top seven FDA-approved drugs with potential binding affinities were selected based on docking scores and subjected to ADMET profiling using pkCSM and SwissADME. The binding of the ADMET-favorable FDA-approved drugs to NLRP3 was validated using MMGBSA (Prime) and Molecular Dynamics (Desmond) in the Schrödinger suite. ADMET profiling revealed that of the seven best docking drugs, empagliflozin and citicoline had good drug-likeness properties. Moreover, MMGBSA analysis and molecular dynamics demonstrated that empagliflozin and citicoline exhibited stable ligand-NLRP3 interactions in the presence of solvents. This study sheds light on the ability of various FDA-approved drugs to act as NLRP3 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vipul Agarwal
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Rajesh Haldhar
- School of Chemical Engineering, Yeungnam University, Gyeongsan, Republic of Korea
| | - Abdurahman Hajinur Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bilal Ahmed
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Sang Beom Han
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Anugya Gupta
- Faculty of Medical and Paramedical Sciences, Madhyanchal Professional University, Bhopal, Madhya Pradesh, India
| | - Vinit Raj
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Sangkil Lee
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
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5
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Vamshi G, D S N B K P, Sampath A, Dammalli M, Kumar P, B S G, Pasala PK, Somasekhar G, Challa MC, Alluril R, Narala VR. Possible cerebroprotective effect of citronellal: molecular docking, MD simulation and in vivo investigations. J Biomol Struct Dyn 2024; 42:1208-1219. [PMID: 37286367 DOI: 10.1080/07391102.2023.2220025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/28/2023] [Indexed: 06/09/2023]
Abstract
This study focused on molecular docking, dynamic simulation, and in vivo approaches to examine the molecular interactions between citronellal (CT) and neurotoxic proteins. In silico studies of CT were performed using proteins involved in the pathophysiology of stroke, such as interleukin-6 (IL-6), interleukin-12 (IL-12), TNF-α, and nitric oxide synthase (NOS), to determine the binding affinity based on their interactions. The docking results of CT revealed that, among the targets, NOS had a better binding energy of -6.4 Kcal/mol. NOS showed good hydrophobic interactions: TYR A, 347; VAL A, 352; PRO A, 350; TYR A, 373 amino acids. Interactions with IL-6, TNF-α, and IL-12 resulted in lower binding affinities of -3.7, -3.9 and -3.1 Kcal/mol. Based on molecular dynamics simulations of 100 ns, the binding affinity of CT (-66.782 ± 7.309 kJ/mol) was well complemented, and NOS stability at the docked site was confirmed. In in vivo studies, cerebral stroke was induced by occlusion of the bilateral common carotid arteries for 30 min and reperfusion for 4 h. CT treatment protected the brain by decreasing cerebral infarction size, increasing GSH(p < 0.001***), decreasing MPO (p < 0.001***), MDA (p < 0.001***), NO production (p < 0.01**), and AChE (p < 0.001***) compared to stroke rats. Histopathological examination revealed that CT treatment reduced the severity of cerebral damage. The investigation concluded that CT strongly binds to NOS, as observed in molecular docking and dynamic simulation studies, which are involved in nitric oxide production, leading to cerebral damage, and CT treatment reduces NO production and oxidative stress parameters, and increases antioxidants via inhibition of NOS function.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- G Vamshi
- SKU College of Pharmaceutical Sciences, SKU, Ananthapuramu, Andhra Pradesh, India
| | - Prasanth D S N B K
- Department of Pharmacognosy, KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh, India
| | - A Sampath
- Department of QA, EQRX International Inc, Cambridge, Massachusetts, USA
| | - Manjunath Dammalli
- Department of Biotechnology, Siddaganga Institute of Technosslogy, Tumkur, Karnataka, India
| | - Pankaj Kumar
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Mangaluru, India
| | - Gowrishankar B S
- Department of Biotechnology, Siddaganga Institute of Technosslogy, Tumkur, Karnataka, India
| | | | - G Somasekhar
- SKU College of Pharmaceutical Sciences, SKU, Ananthapuramu, Andhra Pradesh, India
| | | | - Ramesh Alluril
- Vishnu Institute of Pharmaceutical Education & Research, Medak, Telangana, India
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6
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Alotaibi MO, Alotaibi NM, Alwaili MA, Alshammari N, Adnan M, Patel M. Natural sapogenins as potential inhibitors of aquaporins for targeted cancer therapy: computational insights into binding and inhibition mechanism. J Biomol Struct Dyn 2024:1-22. [PMID: 38174738 DOI: 10.1080/07391102.2023.2299743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Aquaporins (AQPs) are membrane proteins that facilitate the transport of water and other small molecules across biological membranes. AQPs are involved in various physiological processes and pathological conditions, including cancer, making them as potential targets for anticancer therapy. However, the development of selective and effective inhibitors of AQPs remains a challenge. In this study, we explored the possibility of using natural sapogenins, a class of plant-derived aglycones of saponins with diverse biological activities, as potential inhibitors of AQPs. We performed molecular docking, dynamics simulation and binding energy calculation to investigate the binding and inhibition mechanism of 19 sapogenins against 13 AQPs (AQP0-AQP13) that are overexpressed in various cancers. Our results showed that out of 19 sapogenins, 8 (Diosgenin, Gitogenin, Tigogenin, Ruscogenin, Yamogenin, Hecogenin, Sarsasapogenin and Smilagenin) exhibited acceptable drug-like characteristics. These sapogenin also exhibited favourable binding affinities in the range of -7.6 to -13.4 kcal/mol, and interactions within the AQP binding sites. Furthermore, MD simulations provided insights into stability and dynamics of the sapogenin-AQP complexes. Most of the fluctuations in binding pocket were observed for AQP0-Gitogenin and AQP4-Diosgenin. However, remaining protein-ligand complex showed stable root mean square deviation (RMSD) plots, strong hydrogen bonding interactions, stable solvent-accessible surface area (SASA) values and minimum distance to the receptor. These observations suggest that natural sapogenin hold promise as novel inhibitors of AQPs, offering a basis for the development of innovative therapeutic agents for cancer treatment. However, further validation of the identified compounds through experiments is essential for translating these findings into therapeutic applications.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Modhi O Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nahaa M Alotaibi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Maha Abdullah Alwaili
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mitesh Patel
- Research and Development Cell, Department of Biotechnology, Parul Institute of Applied Sciences, Parul University, Vadodara, India
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Yernale NG, Suliphuldevara Mathada B, Shivprasad S, Hiremath S, Karunakar P, Venkatesulu A. Spectroscopic, theoretical and computational investigations of novel benzo[b]thiophene based ligand and its M(II) complexes: As high portentous antimicrobial and antioxidant agents. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123114. [PMID: 37454435 DOI: 10.1016/j.saa.2023.123114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
The reaction of 3-chlorobenzo[b]thiophene-2-carbohydrazide with 4-(diethylamino) salicylaldehyde gave the new ligand; 3-chloro-N'-(4-(diethylamino)-2-hydroxybenzylidene)-benzo[b]thiophene-2-carbohydrazide. The Cu(II), Co(II), Ni(II), and Zn(II) complexes have been successfully prepared. The ligand and the complexes were characterized by analytical, FT-IR, 1H NMR, mass, UV-visible spectroscopy, molar conductivity, and magnetic susceptibility measurements. The FT-IR spectral data showed that the ligand adopted a tridentate fashion when binding with the metal ions via the nitrogen atoms of the imine (C = N), carboxyl (C = O), and phenolic oxygen (O-H) donor atoms. Density Functional Theory (DFT) estimations for the ligand at the DFT/B3LYP level via 6-31G++ (d, p) replicate the structure and geometry. Finally, HOMO and LUMO analyses were used for the charge transfer interface of the structure. Furthermore, molecular docking and ADME calculations were also performed to correlate and interpret the experimental results. The antimicrobial activity study illustrated enhancement in the activity of the free ligand upon complex formation, and the Cu(II) complex (MIC 25 µg mL-1) may be considered a promising antibacterial agent, and the Ni(II) and Zn(II) complexes (MIC 25 µg mL-1) as promising antifungal agents. Also, synthesized Cu(II) and Zn(II) metal complexes (MIC 3.125 µg mL-1) showed promising anti-TB activity against M. tuberculosis. Further, benzo[b]thiophene-based ligand and its metal complexes were evaluated for in vitro antioxidant activity, and in silico docking studies were carried out against Cytochrome c Peroxidase (PDB ID: 2X08).
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Affiliation(s)
| | | | - Swami Shivprasad
- Department of Chemistry, Guru Nanak First Grade College, Bidar, Karnataka, India
| | - Sunilkumar Hiremath
- Department of Chemistry, Guru Nanak First Grade College, Bidar, Karnataka, India
| | - Prashantha Karunakar
- Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Kumaraswamy Layout, Bangalore 560111, Karnataka, India
| | - Adavala Venkatesulu
- Department of PG Studies and Research Centre in Physics, Govt. First Grade College, Hosakote, Bangalore Rural, Karnataka, India
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8
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Poleboyina SM, Poleboyina PK, Pawar SC, Guntuku G. Homology Modeling, Screening, and Identification of Potential FOXO6 Inhibitors Curtail Gastric Cancer Progression: an In Silico Drug Repurposing Approach. Appl Biochem Biotechnol 2023; 195:7708-7737. [PMID: 37086375 DOI: 10.1007/s12010-023-04490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Gastric cancer is the world's second leading cause of cancer-related fatalities, with the epidemiology changing over the previous several decades. FOXOs are the O subfamily of the forkhead box (FOX) transcription factor family, which consists of four members: FOXO1, FOXO3, FOXO4, and FOXO6. FOXO6 mRNA and protein levels are increased in gastric cancer tissues. FOXO6 forced overexpression enhances gastric cancer cell growth, while knockdown decreases proliferation. In our study, the GEPIA, Kaplan-Meier, KEGG, and STRING databases were used to determine FOXO6 mRNA expression, overall survival ratio, interactive pathways, and top 10 associated proteins in gastric cancer respectively. Due to the lack of a solved structure for FOXO6, homology modeling was performed to obtain a 3D structure model, and we used anti-cancer drugs and small molecules to target FOXO6 for identifying a potential selective FOXO6 inhibitor. The chemical composition of the proteins and ligands has a significant impact on docking procedure performance. With this in mind, a critical evaluation of the performance of three regularly used docking routines was carried out: MVD, AutoDock Vina in PyRx, and ArgusLab. The binding affinities, docking scores, and intermolecular interactions were used as assessment criteria. In the study, the porfimer sodium showed excellent binding affinity to the FOXO6 protein. The major three docking software packages were used to analyze the scoring/H-bonding energy and intermolecular interactions. Based on the results, we concluded that FOXO6 was upregulated in gastric cancer and the ligand porfimer sodium emerges as a promising potential FOXO6 inhibitor to curtail gastric cancer progression.
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Affiliation(s)
- Sneha Malleswari Poleboyina
- Department of Pharmaceutical Biotechnology, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India
| | - Pavan Kumar Poleboyina
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India
| | - Smita C Pawar
- Department of Genetics & Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana, 500007, India.
| | - Girijasankar Guntuku
- Department of Pharmaceutical Biotechnology, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, Andhra Pradesh, 530003, India.
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Bathula S, Sankaranarayanan M, Malgija B, Kaliappan I, Bhandare RR, Shaik AB. 2-Amino Thiazole Derivatives as Prospective Aurora Kinase Inhibitors against Breast Cancer: QSAR, ADMET Prediction, Molecular Docking, and Molecular Dynamic Simulation Studies. ACS OMEGA 2023; 8:44287-44311. [PMID: 38027360 PMCID: PMC10666282 DOI: 10.1021/acsomega.3c07003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/05/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The aurora kinase is a key enzyme that is implicated in tumor growth. Research revealed that small molecules that target aurora kinase have beneficial effects as anticancer agents. In the present study, in order to identify potential antibreast cancer agents with aurora kinase inhibitory activity, we employed QSARINS software to perform the quantitative structure-activity relationship (QSAR). The statistical values resulted from the study include R2 = 0.8902, CCCtr = 0.7580, Q2 LOO = 0.7875, Q2LMO = 0.7624, CCCcv = 0.7535, R2ext = 0.8735, and CCCext = 0.8783. Among the four generated models, the two best models encompass five important variables, including PSA, EstateVSA5, MoRSEP3, MATSp5, and RDFC24. The parameters including the atomic volume, atomic charges, and Sanderson's electronegativity played an important role in designing newer lead compounds. Based on the above data, we have designed six series of compounds including 1a-e, 2a-e, 3a-e, 4a-e, 5a-e, and 6a-e. All these compounds were subjected to molecular docking studies by using AutoDock v4.2.6 against the aurora kinase protein (1MQ4). Among the above 30 compounds, the 2-amino thiazole derivatives 1a, 2a, 3e, 4d, 5d, and 6d have excellent binding interactions with the active site of 1MQ4. Compound 1a had the highest docking score (-9.67) and hence was additionally subjected to molecular dynamic simulation investigations for 100 ns. The stable binding of compound 1a with 1MQ4 was verified by RMSD, RMSF, RoG, H-bond, molecular mechanics-generalized Born surface area (MM-GBSA), free binding energy calculations, and solvent-accessible surface area (SASA) analyses. Furthermore, newly designed compound 1a exhibited excellent ADMET properties. Based on the above findings, we propose that the designed compound 1a may be utilized as the best theoretical lead for future experimental research of selective inhibition of aurora kinase, therefore assisting in the creation of new antibreast cancer drugs.
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Affiliation(s)
- Sivakumar Bathula
- Department
of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM
Institute of Science and Technology, Kattankulathur 603203, Chengalpattu
District, Tamil Nadu, India
| | - Murugesan Sankaranarayanan
- Medicinal
Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science (BITS)
Pilani, Pilani Campus, Pilani 333031, Rajasthan, India
| | - Beutline Malgija
- MCC-MRF
Innovation Park, Madras Christian College, Chennai 600059, Tamil Nadu, India
| | - Ilango Kaliappan
- Department
of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM
Institute of Science and Technology, Kattankulathur 603203, Chengalpattu
District, Tamil Nadu, India
| | - Richie R. Bhandare
- Department
of Pharmaceutical Sciences, College
of Pharmacy and Health Sciences, Ajman University, P.O. Box 346, Ajman 61001, United Arab Emirates
- Centre of
Medical and Bio-allied Health Sciences Research, Ajman University, P.O. Box 346, Ajman 61001, United Arab Emirates
| | - Afzal B. Shaik
- St.
Mary’s College of Pharmacy, St. Mary’s
Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological
University Kakinada, Chebrolu, Guntur 522212, Andhra
Pradesh, India
- Center
for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India
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10
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Nayila I, Sharif S, Lodhi MS, Rehman MFU, Aman F. Synthesis, characterization and anti-breast cancer potential of an incensole acetate nanoemulsion from Catharanthus roseus essential oil; in silico, in vitro, and in vivo study. RSC Adv 2023; 13:32335-32362. [PMID: 37928847 PMCID: PMC10621725 DOI: 10.1039/d3ra06335f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
The characteristics of phytocompounds and essential oils have undergone extensive research in the medical and pharmaceutical sectors due to their extensive usage. In spite of the fact that these molecules are widely used, terpenes, terpenoids, and their derivatives have not yet been well characterized. This study intends to evaluate the prospective activity of incensole acetate (IA), a compound identified and isolated from Catharanthus roseus essential oil by GC/MS analysis and column chromatography, and to analyze the anticancer effect of an IA biosynthesized nanoemulsion against breast cancer. The in silico activity of IA against breast cancer targets was observed by molecular docking, ADMET assessment and molecular dynamics simulations. The IA-mediated nanoformulation exhibited cytotoxicity against breast cancer cell lines at an effective concentration when analyzed by MTT and crystal violet assay. The increased interleukin serum indicators were significantly improved as a result of nanoemulsion treatment in a DMBA-induced rat model. In addition, the anticancer properties of IA biosynthesized nanoemulsion are supported due to their potential effects on biochemical parameters, oxidative stress markers, proinflammatory cytokines, and upon tumor growth profiling in cancer-induced rats.
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Affiliation(s)
- Iffat Nayila
- Institute of Molecular Biology and Biotechnology, The University of Lahore Lahore Pakistan
| | - Sumaira Sharif
- Institute of Molecular Biology and Biotechnology, The University of Lahore Lahore Pakistan
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology, The University of Lahore Lahore Pakistan
| | | | - Farhana Aman
- Department of Chemistry, The University of Lahore Sargodha Campus Sargodha Pakistan
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11
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Suresh Babu AR, Sharma A, Athira MP, Alajangi HK, Naresh Raj AR, Gartia J, Singh G, Barnwal RP. Evaluation of antibiofilm properties of dehydroacetic acid (DHA) grafted spiro-oxindolopyrrolidines synthesized via multicomponent 1,3-dipolar cycloaddition reaction. Sci Rep 2023; 13:15289. [PMID: 37714933 PMCID: PMC10504327 DOI: 10.1038/s41598-023-42528-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023] Open
Abstract
The current work involves the use of dehydroacetic acid based chalcone derivatives for the synthesis of spirooxindole grafted pyrrolidine moieties. All the synthesized compounds have been characterized using spectroscopic techniques such as NMR (1H-NMR and 13C-NMR), IR, mass and elemental analysis. Molecular mechanics studies were performed to comprehend the regioselectivity in the product formation. Molecular docking of the synthesized compounds was performed with few bacterial proteins of Bacillus subtilis and Pseudomonas aeruginosa responsible for biofilm formation followed by molecular dynamics simulations with the potential lead compound. Further, to corroborate the results obtained via in silico study, anti-biofilm activity etc. of the synthesized compounds (4a-e) was checked for effectiveness against biofilm formation. Taken together, this study opens up to explore these compounds' multiple roles in diverse fields in the arena of medical sciences.
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Affiliation(s)
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh, 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - M P Athira
- Department of Chemistry, IISER, Mohali, Sahibzada Ajit Singh Nagar, Punjab, 140306, India
| | - Hema K Alajangi
- Department of Biophysics, Panjab University, Chandigarh, 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - A R Naresh Raj
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College, Arumbakkam, Chennai, 600106, India
| | - Janeka Gartia
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, Odisha, 751024, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India.
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Bhowmik P, Baezid HM, Arabi II. Assessment of antidiabetic activity of three Phenylspirodrimanes from fungus Stachybotrys chartarum MUT 3308 by ADME, QSAR, molecular docking and molecular dynamics simulation studies against protein tyrosine phosphatase 1B (PTP1B). J Biomol Struct Dyn 2023:1-15. [PMID: 37698508 DOI: 10.1080/07391102.2023.2256410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Phenylspirodrimanes (PSD) are the sesquiterpene quinone type meroterpenoids found in nature. PSDs are found to exhibit inhibitory activity against immunocomplex diseases, and tyrosine kinase receptors. Three of the different PSDs C1, C2, and C3 that have been reported to be isolated from the sponge-associated fungus Stachybotrys chartarum MUT 3308 are selected for studying their possible inhibitory effect against type 2 diabetes mellitus. Mechanistically, blocking protein tyrosine phosphatase 1B (PTP1B) helps to reduce the insulin resistance induction caused by the high expression of PTP1B. The QSAR, ADME, toxicity (T) study was carried out to predict the pharmacokinetic properties and the biological activities of the PSDs. PASS prediction web tool was used to find and select the target proteins 1NNY, and 2HNP. According to the molecular docking simulations, C1 and C2 showed better binding affinity of -8.5 kcal/mol, and -8.1 kcal/mol respectively against 1NNY compared to the control ligand. RMSD, RMSF, Rg, and SASA analysis revealed that both C1, and C2 showed better stability, minor conformational changes, and minor fluctuation upon binding to PTP1B. Protein contact analysis was carried out to validate the residues that are in contact with the ligands according to molecular docking studies. Overall, C1, and C2 could be proposed as novel natural hits to be developed and small modifications of these PSDs could result in inducing the binding affinity significantly, although experimental validation is required for further evaluation of the work.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prasenjit Bhowmik
- Department of Chemistry-BMC, Biochemistry, Disciplinary Domain of Science and Technology, Uppsala University, Uppsala, Sweden
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
- Department of Textile Engineering, Green University of Bangladesh, Narayanganj, Bangladesh
| | - Hossain Mohammad Baezid
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Ishmam Ibnul Arabi
- Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, Bangladesh
- Department of Textile Engineering, Green University of Bangladesh, Narayanganj, Bangladesh
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Pingili D, Svum P, Nulgumnalli Manjunathaiah R. Design, Synthesis, In‐silico Studies and Antiproliferative Evaluation of Novel Indazole Derivatives as Small Molecule Inhibitors of B‐Raf. ChemistrySelect 2023. [DOI: 10.1002/slct.202300291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Divya Pingili
- Department of Pharmaceutical Chemistry Sri Venkateshwara College of Pharmacy Madhapur, Hyderabad 500081 Telangana India
- Department of Pharmacy Jawaharlal Nehru Technological University, postCode/>533003 Kakinada Andhrapradesh India
| | - Prasad Svum
- Department of Pharmacy Jawaharlal Nehru Technological University, postCode/>533003 Kakinada Andhrapradesh India
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Asif M, Aqil F, Alasmary FA, almalki AS, Khan AR, Nasibullah M. Lewis base-catalyzed synthesis of highly functionalized spirooxindole-pyranopyrazoles and their in vitro anticancer studies. Med Chem Res 2023. [DOI: 10.1007/s00044-023-03053-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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15
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In Silico Identification of Peptides with PPARγ Antagonism in Protein Hydrolysate from Rice (Oryza sativa). Pharmaceuticals (Basel) 2023; 16:ph16030440. [PMID: 36986539 PMCID: PMC10057873 DOI: 10.3390/ph16030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/04/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
At least half the population in industrialized countries suffers from obesity due to excessive accumulation of adipose tissue. Recently, rice (Oryza sativa) proteins have been considered valuable sources of bioactive peptides with antiadipogenic potential. In this study, the digestibility and bioaccessibility in vitro of a novel protein concentrate (NPC) from rice were determined through INFOGEST protocols. Furthermore, the presence of prolamin and glutelin was evaluated via SDS-PAGE, and their potential digestibility and the bioactivity of ligands against peroxisome proliferator-activated receptor gamma (PPARγ) were explored by BIOPEP UWM and HPEPDOCK. For the top candidates, molecular simulations were conducted using Autodock Vina to evaluate their binding affinity against the antiadipogenic region of PPARγ and their pharmacokinetics and drug-likeness using SwissADME. Simulating gastrointestinal digestion showed a recovery of 43.07% and 35.92% bioaccessibility. The protein banding patterns showed the presence of prolamin (57 kDa) and glutelin (12 kDa) as the predominant proteins in the NPC. The in silico hydrolysis predicts the presence of three and two peptide ligands in glutelin and prolamin fraction, respectively, with high affinity for PPARγ (≤160). Finally, the docking studies suggest that the prolamin-derived peptides QSPVF and QPY (−6.38 & −5.61 kcal/mol, respectively) have expected affinity and pharmacokinetic properties to act as potential PPARγ antagonists. Hence, according to our results, bioactive peptides resulting from NPC rice consumption might have an antiadipogenic effect via PPARγ interactions, but further experimentation and validation in suitable biological model systems are necessary to gain more insight and to provide evidence to support our in silico findings.
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In Silico, In Vitro, and Ex Vivo Biological Activity of Some Novel Mebeverine Precursors. Biomedicines 2023; 11:biomedicines11020605. [PMID: 36831141 PMCID: PMC9953468 DOI: 10.3390/biomedicines11020605] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a functional gastroenterological disorder with complex pathogenesis and multifaceted therapy approaches, aimed at alleviating clinical symptoms and improving the life quality of patients. Its treatment includes dietary changes and drugs from various pharmacological groups such as antidiarrheals, anticholinergics, serotonin receptor antagonists, targeting chloride ion channels, etc. The present article is focused on the synthesis and biological evaluation of some mebeverine precursors as potential antispasmodics. METHODS In silico analysis aimed at predicting the pharmacodynamic profile of the compounds was performed. Based on these predictions, ex vivo bioelectrical activity (BEA) and immunohistochemical effects of the compounds were established. A thorough biological evaluation of the compounds was conducted assessing their in vitro antimicrobial and cytotoxic activity. RESULTS All the newly synthesized compounds exerted drug-like properties, whereby 3-methyl-1-phenylbutan-2-amine 3 showed a significant change in BEA due to Ca2+ channel regulation, Ca2+ influx modulation, and a subsequent change in smooth muscle cell response. The immunohistochemical studies showed a good correlation with the obtained data on the BEA, defining amine 3 as a leader structure. No cytotoxicity to human malignant leukemic cell lines (LAMA-84, K-562) was observed for all tested compounds. CONCLUSION Based on the experimental results, we outlined 3-methyl-1-phenylbutan-2-amine 3 as a potential effective choice for orally active long-term therapy of IBS.
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Sun L, Zhang M, Xie L, Xu X, Xu P, Xu L. Computational prediction of Lee retention indices of polycyclic aromatic hydrocarbons by using machine learning. Chem Biol Drug Des 2023; 101:380-394. [PMID: 36102275 DOI: 10.1111/cbdd.14137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/28/2022] [Indexed: 01/14/2023]
Abstract
Given the difficult of experimental determination, quantitative structure-property relationship (QSPR) and deep learning (DL) provide an important tool to predict physicochemical property of chemical compounds. In this paper, partial least squares (PLS), genetic function approximation (GFA), and deep neural network (DNN) were used to predict the Lee retention index (Lee-RI) of PAHs in SE-52 and DB-5 stationary phases. Four molecular descriptors, molecular weight (MW), quantitative estimate of drug-likeness (QED), atomic charge weighted negative surface area (Jurs_PNSA_3), and relative negative charge (Jurs_RNCG) were selected to construct regression models based on genetic algorithm. For SE-52, PLS model showed best prediction power, followed by DNN and GFA. The relative error (RE), root mean square error (RMSE), and regression coefficient (R2 ) of best PLS regression model are 1.228%, 5.407, and 0.980. For DB-5, DNN model showed best prediction power, followed by GFA and PLS. The RE, RMSE and R2 of best DNN regression model for DB-5-1 and DB-5-2 are 1.058%, 4.325%, 0.976%, 0.821%, 3.795%, and 0.970%, respectively. The three regression models not only show good predictive ability, but also highlight the stability and ductility of the models.
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Affiliation(s)
- Linkang Sun
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Min Zhang
- School of Computer Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Peng Xu
- Department of Orthopedics, Second Military Medical University Affiliated Changzheng Hospital, Shanghai, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
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Nuha D, Evren AE, Kapusiz Ö, Gül ÜD, Gundogdu-Karaburun N, Karaburun AÇ, Berber H. Design, synthesis, and antimicrobial activity of novel coumarin derivatives: An in-silico and in-vitro study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Roy S, Sen S, Saha S, Deb SK, Singh B, Biswas G. Design, synthesis and molecular docking studies of 5-fluoro 1-aryl/alkyl sulfonyl benzimidazole derivatives for treatment of Parkinson’s disease. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2150852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Subarna Roy
- Department of Chemistry, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal, India
| | - Subhadeep Sen
- Department of Chemistry, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal, India
| | - Samiran Saha
- Department of Chemistry, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal, India
| | - Sandip Kumar Deb
- Department of Chemistry, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal, India
| | - Bhagat Singh
- Department of Chemistry and Biochemistry, University of North Carolina, Greensboro, NC, USA
| | - Goutam Biswas
- Department of Chemistry, Cooch Behar Panchanan Barma University, Cooch Behar, West Bengal, India
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Pangal A, Ahmed K. Synthesis and biological evaluation of coumarin-quinone hybrids as multifunctional bioactive agents. ADMET & DMPK 2022; 11:81-96. [PMID: 36778907 PMCID: PMC9909729 DOI: 10.5599/admet.1468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/29/2022] [Indexed: 11/18/2022]
Abstract
We report the synthesis, structural characterization and pharmaceutical activity of four coumarin-quinone hybrids. The compounds were significantly active against Staphylococcus aureus, Pseudomonas aeoginosa and Candida albicans. Promising antioxidant activity was observed when compared to ascorbic acid. Two compounds, DTBSB and DTBSN, also showed commendable in vitro antiproliferative activities against the cells of human cancer cell lines MCF-7, MDA-MB-231, COLO-205, HT-29 and A549 along with appreciable tumor selectivity with distinct selectivity index. Molecular docking studies using cyclooxygenase-2 (PDB ID: 6COX) revealed strong binding affinities for the COX-2 active site. Moreover, ADMET properties of the synthesized compounds were determined using the pKCSM and SwissADME online tools and all the compounds had accurate pharmacokinetic profiles. Hence, the new coumarin-quinone hybrids DTBSB and DTBSN can be considered for optimization and lead development.
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Affiliation(s)
- Anees Pangal
- Department of Chemistry & Post Graduate Centre, Abeda Inamdar Sr. College of Arts, Science & Commerce (Autonomous), Camp, Pune – 411001, India,Advanced Scientific Research Laboratory, Azam Campus, Pune – 411001, India
| | - Khursheed Ahmed
- Department of Chemistry & Post Graduate Centre, Abeda Inamdar Sr. College of Arts, Science & Commerce (Autonomous), Camp, Pune – 411001, India,Advanced Scientific Research Laboratory, Azam Campus, Pune – 411001, India,*Corresponding Author: E-mail:
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21
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Coordination Chemistry, Antibacterial Screening, and In Silico ADME Study of Mononuclear NiII and CuII Complexes of Asymmetric Schiff Base of Streptomycin and Aniline. J CHEM-NY 2022. [DOI: 10.1155/2022/3881217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel metal complexes, that is, Ni (StmAn)2(4) and Cu (StmAn)2(5), were synthesized from unsymmetrical Schiff base ligand StmAn (3). The ligand was prepared by refluxing streptomycin (2) and aniline (1). They were characterized by elemental microanalysis, conductivity measurements, and spectroscopic techniques such as 1H NMR, FT-IR, ESI-mass, and electronic absorption spectral study. Interestingly, the study revealed metal coordination through azomethine nitrogen and N-atom of NH-CH3 of N-methyl-L-glucosamine unit of streptomycin. The electronic absorption spectral study supported an octahedral geometry for complex 4 and a tetrahedral geometry for complex 5. Particle size calculation by Scherrer’s formula indicated their nanocrystalline nature. The geometry optimization of the complexes was achieved by running an MM2 job in Gaussian supported Cs-ChemOffice ultra-12.0.1 and ArgusLab 4.0.1 version software. Based on SwissADME predictions, a theoretical drug profile was generated by analyzing absorption, distribution, metabolism, excretion, and toxicity (ADMET) scores of the compounds. They were screened for in vitro antibacterial activity study against four clinical pathogens such as E. coli, S. pneumoniae, P. vulgaris, and S. aureus. Minimum inhibitory concentration (MIC) study demonstrated greater inhibitory potency of complex (4) (0.024 g/L) for S. aureus relative to ligand (3) and complex (5). Studies show that metal complexes are more toxic to bacteria.
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22
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Bakchi B, Krishna AD, Sreecharan E, Ganesh VBJ, Niharika M, Maharshi S, Puttagunta SB, Sigalapalli DK, Bhandare RR, Shaik AB. An overview on applications of SwissADME web tool in the design and development of anticancer, antitubercular and antimicrobial agents: A medicinal chemist's perspective. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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23
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Design, synthesis and docking study of Vortioxetine derivatives as a SARS-CoV-2 main protease inhibitor. DARU : JOURNAL OF FACULTY OF PHARMACY, TEHRAN UNIVERSITY OF MEDICAL SCIENCES 2022; 30:139-152. [PMID: 35508799 PMCID: PMC9067898 DOI: 10.1007/s40199-022-00441-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/09/2022] [Indexed: 12/02/2022]
Abstract
Purpose Vortioxetine an anti-depressant FDA-drug recently reported showing better in vitro efficacy against SARS-CoV-2. Methods In this study, we have synthesized ten new derivatives having alkenes, alkynes, benzyl, aryl, and mixed carbamate at the N-terminal of vortioxetine. Then the binding energy and interactions with the crucial amino acid residues in the binding pocket of main protease (Mpro) of SARS-CoV-2, of reported and ten newly synthesized vortioxetine derivatives (total thirty-one) in comparison with remdesivir are analyzed and presented in this paper. Results Based on the docking scores predicted by ADV and AD, most vortioxetine derivatives showed better binding efficiency towards Mpro of SARS-CoV-2 in comparison with remdesivir (an EUA approved drug against SARS-CoV-2 Mpro) and vortioxetine. Conclusion This study shows that some vortioxetine derivatives can be developed into promising drugs for COVID-19 treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s40199-022-00441-z.
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Nuha D, Evren AE, Çiyanci ZŞ, Temel HE, Akalin Çiftçi G, Yurttaş L. Synthesis, density functional theory calculation, molecular docking studies, and evaluation of novel 5-nitrothiophene derivatives for anticancer activity. Arch Pharm (Weinheim) 2022; 355:e2200105. [PMID: 35584987 DOI: 10.1002/ardp.202200105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 12/29/2022]
Abstract
Within the scope of this study, new 2-{2-[(5-nitrothiophen-2-yl)methylene]hydrazinyl}thiazole derivatives (2a-j) were synthesized and investigated for their potential anticancer and enzyme inhibition activities. Spectroscopic techniques were used to determine the structures of substances. The anticancer activities of compounds were detected in A549 human lung carcinoma and L929 murine fibroblast cell lines, determining cytotoxicity, apoptosis, mitochondrial membrane integrity, and caspase-3 activation. Compounds 2b bearing 4-nitrophenyl, 2c bearing phenyl, and 2d bearing 4-cyanophenyl moieties were specified with high anticancer activity, acting through an apoptotic pathway with an apoptosis ratio of 9.61%-15.59%. Mitochondrial membrane depolarization was determined to be 25.53% and 22.33% for compounds 2b and 2c, respectively. Furthermore, compound 2c exhibited excellent caspase-3 activation. A molecular docking study was realized with compound 2c on the caspase-3 enzyme. Furthermore, the electronic characteristics of the active compounds were investigated using density functional theory (DFT) at the B3LYP/6-31G (d, p) level. The frontier molecular orbital energy and atomic net charges were examined.
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Affiliation(s)
- Demokrat Nuha
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey.,Department of Chemistry, Faculty of Science, Eskisehir Technical University, Eskişehir, Turkey.,Faculty of Pharmacy, University of Business and Technology, Prishtina, Kosovo
| | - Asaf E Evren
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey.,Department of Pharmacy Services, Vocational School of Health Services, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Zennure Ş Çiyanci
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Halide E Temel
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Gülşen Akalin Çiftçi
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Leyla Yurttaş
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
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25
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Rayff da Silva P, Diniz Nunes Pazos N, Karla Silva do Nascimento Gonzaga T, Cabral de Andrade J, Brito Monteiro Á, Caroline Ribeiro Portela A, Fernandes Oliveira Pires H, Dos Santos Maia M, Vilar da Fonsêca D, T Scotti M, Maria Barbosa Filho J, Pergentino de Sousa D, Francisco Bezerra Felipe C, Nóbrega de Almeida R, Scotti L. Anxiolytic and antidepressant-like effects of monoterpene tetrahydrolinalool and in silico approach of new potential targets. Curr Top Med Chem 2022; 22:1530-1552. [PMID: 35524664 DOI: 10.2174/1568026622666220505104726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/03/2022] [Accepted: 02/16/2022] [Indexed: 11/22/2022]
Abstract
INTRODUCTION- The drugs currently available for treatment of anxiety and depression act through modulation of the neurotransmission systems involved in the neurobiology of the disorder, yet they of-ten present side effects, which can impair patient adherence to treatment. METHOD- This, has driven the search for new molecules with anxiolytic and antidepressant potential. Aromatic plants are rich in essential oils, and their chemical constituents, such as monoterpenes, are be-ing studied for these disorders. This study aims to evaluate the anxiolytic and antidepressant-like poten-tial of the monoterpene tetrahydrolinalool in in vivo animal models, and review pharmacological targets with validation through molecular docking. Male Swiss mice (Mus musculus) were treated with THL (37.5-600 mg kg-1 p.o.) and submitted to the elevated plus maze, open field, rota rod, and forced swim tests. In the elevated plus-maze, THL at doses of 37.5 and 75 mg kg-1 induced a significant increase in the percentage of entries (72.7 and 64.3% respectively), and lengths of stay (80.3 and 76.8% respective-ly) in the open arms tests. RESULT- These doses did not compromise locomotor activity or motor coordination in the animals. In the open field, rota rod tests, and the forced swimming model, treatment with THL significantly reduced immobility times at doses of 150, 300, and 600 mg kg-1, and by respective percentages of 69.3, 60.9 and 68.7%. CONCLUSION- In molecular docking assay, which investigated potential targets, THL presented sat-isfactory energy values for: nNOs, SGC, IL-6, 5-HT1A, NMDAr, and D1. These demonstrate the po-tential of THL (a derivative of natural origin) in in vivo and in silico models, making it a drug candidate.
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Affiliation(s)
- Pablo Rayff da Silva
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Natalia Diniz Nunes Pazos
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | | | - Jéssica Cabral de Andrade
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Álefe Brito Monteiro
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Anne Caroline Ribeiro Portela
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Hugo Fernandes Oliveira Pires
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Mayara Dos Santos Maia
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-900, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Diogo Vilar da Fonsêca
- Collegiate of Medicine, Federal University of São Francisco Valley, 48607-190, Rua Aurora, S/N, Bahia, Brazil
| | - Marcus T Scotti
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-900, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - José Maria Barbosa Filho
- Pharmaceutical Chemistry Laboratory, Department of Pharmaceutical Sciences, Federal University of Paraíba, 58051-900, Via Ipê Amarelo, S/N, João Pessoa, Brazil
| | - Damião Pergentino de Sousa
- Pharmaceutical Chemistry Laboratory, Department of Pharmaceutical Sciences, Federal University of Paraíba, 58051-900, Via Ipê Amarelo, S/N, João Pessoa, Brazil
| | - Cícero Francisco Bezerra Felipe
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Reinaldo Nóbrega de Almeida
- Psychopharmacology Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-085, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
| | - Luciana Scotti
- Cheminformatics Laboratory, Institute of Drugs and Medicines Research, Federal University of Paraíba, 58051-900, Via Ipê Amarelo, S/N, João Pessoa, Paraíba, Brazil
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26
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Rudrapal M, Gogoi N, Chetia D, Khan J, Banwas S, Alshehri B, Alaidarous MA, Laddha UD, Khairnar SJ, Walode SG. Repurposing of phytomedicine-derived bioactive compounds with promising anti-SARS-CoV-2 potential: Molecular docking, MD simulation and drug-likeness/ADMET studies. Saudi J Biol Sci 2022; 29:2432-2446. [PMID: 34924801 PMCID: PMC8667520 DOI: 10.1016/j.sjbs.2021.12.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 11/28/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
In view of the potential of traditional plant-based remedies (or phytomedicines) in the management of COVID-19, the present investigation was aimed at finding novel anti-SARS-CoV-2 molecules by in silico screening of bioactive phytochemicals (database) using computational methods and drug repurposing approach. A total of 160 compounds belonging to various phytochemical classes (flavonoids, limonoids, saponins, triterpenoids, steroids etc.) were selected (as initial hits) and screened against three specific therapeutic targets (Mpro/3CLpro, PLpro and RdRp) of SARS-CoV-2 by docking, molecular dynamics simulation and drug-likeness/ADMET studies. From our studies, six phytochemicals were identified as notable ant-SARS-CoV-2 agents (best hit molecules) with promising inhibitory effects effective against protease (Mpro and PLpro) and polymerase (RdRp) enzymes. These compounds are namely, ginsenoside Rg2, saikosaponin A, somniferine, betulinic acid, soyasapogenol C and azadirachtin A. On the basis of binding modes and dynamics studies of protein-ligand intercations, ginsenoside Rg2, saikosaponin A, somniferine were found to be the most potent (in silico) inhibitors potentially active against Mpro, PLpro and RdRp, respectively. The present investigation can be directed towards further experimental studies in order to confirm the anti-SARS-CoV-2 efficacy along with toxicities of identified phytomolecules.
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Affiliation(s)
- Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India
| | - Neelutpal Gogoi
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Saeed Banwas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Bader Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Mohammed A. Alaidarous
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Umesh D. Laddha
- MET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, Maharashtra, India
| | - Shubham J. Khairnar
- MET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, Maharashtra, India
| | - Sanjay G. Walode
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India
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Júniora CRM, Costa ED. Design and Analysis of Pharmacokinetics, Pharmacodynamics and Toxicological analysis of Cannabidiol analogs using in silico Tools. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220202151959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Background: Cannabidiol (CBD), a non‐psychoactive phytocannabinoid from Cannabis Sativa, has become an interesting option for medicinal chemists in the development of new drug candidates
Objective:
Objective: This study aims to propose analogs with therapeutic potential from the CBD scaffold. Methods: The 16 analogs proposed were designed using the PubChem Sketcher V. 2.4® software. Already, CBD analogs were subjected to different in silico tools, such as Molinspiration®; SwissADME®; SwissTargetPrediction® and OSIRIS Property Explorer
Results and Discussio:
Results and Discussion: The screening of CBD analogs carried out in this study showed compounds 9 and 16 with good affinity for interactions with CB1 and CB2 receptors. Pharmacokinetic data showed that these two compounds have good oral absorption. Finally, in silico toxicity data showed that these compounds pose no risk of a toxic event in humans
Conclusion:
Conclusion: CBD analogs 9 and 16 would have a better profile of drug candidates to be further tested in vitro and in vivo models.: CBD analogs 9 and 16 would have a better profile of drug candidates to be further tested in vitro and in vivo models.
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28
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Saigal, Khizr M, Sahoo SC, Khan MM. Synthesis, characterization, X-ray crystallographic study and in silico ADME predictions of functionalized nitropyrrole derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Evren AE, Nuha D, Dawbaa S, Sağlık BN, Yurttaş L. Synthesis of novel thiazolyl hydrazone derivatives as potent dual monoamine oxidase-aromatase inhibitors. Eur J Med Chem 2022; 229:114097. [PMID: 34998057 DOI: 10.1016/j.ejmech.2021.114097] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 12/18/2022]
Abstract
The inhibitory effects of 2-thiazolyl hydrazones on monoamine oxidase enzymes are known for a long time. In this study, a new series of 2-thiazolyl hydrazone derivatives were synthesized starting from 6-methoxy-2-naphthaldehyde. All of the synthesized compounds were investigated in terms of their monoamine oxidase (MAO) inhibitory effects and significant results were found. The results showed that compound 2j potently inhibited MAO-A and MAO-B, while compound 2t strongly and selectively inhibited MAO-B compared to standard drugs. Compounds 2k and 2q exhibited selective and satisfying inhibition on MAO-B. In the aromatase inhibition studies of the compounds, it was determined that compounds 2q and 2u had high inhibitory properties. Molecular docking studies on MAO-A, MAO-B, and aromatase enzymes were carried out for the aforementioned compounds. Additionally, molecular dynamics simulation was studied for compound 2q on MAO-B and aromatase complexes. Finally, the Field-based QSAR study was developed and the structure-activity relationship (SAR) was explained. For the first time, dual inhibitors on MAO and aromatase enzyme were investigated together. The aim of this approach is for finding the potential agents that do not cause the cognitive disorders and may even treat neurodegenerative symptoms, thus, the aim was reached successfully.
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Affiliation(s)
- Asaf Evrim Evren
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey; Bilecik Şeyh Edebali University, Vocational School of Health Services, Department of Pharmacy Services, 11000, Bilecik, Turkey.
| | - Demokrat Nuha
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey; Eskisehir Technical University, Faculty of Science, Department of Chemistry, 26555, Eskişehir, Turkey
| | - Sam Dawbaa
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey; Department of Pharmacy, Faculty of Medicine and Health Sciences, Thamar University, Dhamar, Yemen
| | - Begüm Nurpelin Sağlık
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
| | - Leyla Yurttaş
- Anadolu University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 26470, Eskişehir, Turkey
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30
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In Silico Analysis and Experimental Evaluation of Ester Prodrugs of Ketoprofen for Oral Delivery: With a View to Reduce Toxicity. Processes (Basel) 2021. [DOI: 10.3390/pr9122221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The present research aimed to synthesize ketoprofen prodrugs and to demonstrate their potentiality for oral treatment to treat chronic inflammation by reducing its hepatotoxicity and gastrointestinal irritation. Methyl 2-(3-benzoyl phenyl) propanoate, ethyl 2-(3-benzoyl phenyl) propanoate and propyl 2-(3-benzoyl phenyl) propanoate was synthesized by esterification and identified by nuclear magnetic resonance (1HNMR) and infrared (IR) spectrometric analysis. In silico SwissADME and ProTox-II analysis stated methyl derivative as ideal candidate for oral absorption, having a >30-fold LD50 value compared to ketoprofen with no hepatotoxicity. Moreover, in vivo hepatotoxicity study demonstrates that these ester prodrugs have significantly lower effects on liver toxicity compared to pure ketoprofen. Furthermore, ex vivo intestinal permeation enhancement ratio was statistically significant (* p < 0.05) compared to ketoprofen. Likewise, the prodrugs were found to exhibit not only remarkable in vitro anti-proteolytic and lysosomal membrane stabilization potentials, but also significant efficiency to alleviate pain induced by inflammation, as well as central and peripheral stimulus in mice model in vivo. These outcomes recommend that ketoprofen ester prodrugs, especially methyl derivative, can be a cost-effective candidate for prolonged treatment of chronic inflammatory diseases.
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31
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Azad I, Khan T, Maurya AK, Irfan Azad M, Mishra N, Alanazi AM. Identification of Severe Acute Respiratory Syndrome Coronavirus-2 inhibitors through in silico structure-based virtual screening and molecular interaction studies. J Mol Recognit 2021; 34:e2918. [PMID: 34132436 PMCID: PMC8420533 DOI: 10.1002/jmr.2918] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023]
Abstract
The novel coronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) or COVID-19 has caused a worldwide pandemic. The fatal virus has affected the health of human beings as well as the socio-economic situation all over the world. To date, no concrete medicinal solution has been proposed to combat the viral infection, calling for an urgent, strategic, and cost-effective drug development approach that may be achievable by applying targeted computational and virtual screening protocols. Immunity is the body's natural defense against disease-causing pathogens, which can be boosted by consuming plant-based or natural food products. Active constituents derived from natural sources also scavenge the free radicals and have anti-inflammatory activities. Herbs and spices have been used for various medicinal purposes. In this study, 2,96 365 natural and synthetic derivatives (ligands) belonging to 102 classes of compounds were obtained from PubChem and assessed on Lipinski's parameters for their potential bioavailability. Out of all the derivatives, 3254 obeyed Lipinski's rule and were virtually screened. The 115 top derivatives were docked against SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-HKV1 main proteases (Mpro s) as receptors using AutoDock Vina, AutoDock, and iGEMDOCK 2.1. The lowest binding energy was exhibited by ligands 2 and 6 against all the four Mpro s. The molecular dynamic simulation was also performed with ligand 6 using the GROMACS package. Good bioactivity scores, absorption, distribution, metabolism, excretion, and toxicity profile and drug-like pharmacokinetic parameters were also obtained. Hydroxychloroquine was used as the control drug.
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Affiliation(s)
- Iqbal Azad
- Department of ChemistryIntegral UniversityLucknowIndia
| | - Tahmeena Khan
- Department of ChemistryIntegral UniversityLucknowIndia
| | - Akhilesh Kumar Maurya
- Department of Applied SciencesIndian Institute of Information Technology AllahabadPrayagrajIndia
| | | | - Nidhi Mishra
- Department of Applied SciencesIndian Institute of Information Technology AllahabadPrayagrajIndia
| | - Amer M. Alanazi
- Department of Pharmaceutical ChemistryCollege of Pharmacy, King Saud UniversityRiyadhSaudi Arabia
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32
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Bioactive Antidiabetic Flavonoids from the Stem Bark of Cordia dichotoma Forst.: Identification, Docking and ADMET Studies. MOLBANK 2021. [DOI: 10.3390/m1234] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Cordia dichotoma Forst. (F. Boraginaceae) has been traditionally used for the management of a variety of human ailments. In our earlier work, the antidiabetic activity of methanolic bark extract of C. dichotoma (MECD) has been reported. In this paper, two flavonoid molecules were isolated (by column chromatography) and identified (by IR, NMR and mass spectroscopy/spectrometry) from the MECD with an aim to investigate their antidiabetic effectiveness. Molecular docking and ADMET studies were carried out using AutoDock Vina software and Swiss ADME online tool, respectively. The isolated flavonoids were identified as 3,5,7,3′,4′-tetrahydroxy-4-methoxyflavone-3-O-L-rhamnopyranoside and 5,7,3′-trihydroxy-4-methoxyflavone-7-O-L-rhamnopyranoside (quercitrin). Docking and ADMET studies revealed the promising binding affinity of flavonoid molecules for human lysosomal α-glucosidase and human pancreatic α-amylase with acceptable ADMET properties. Based on computational studies, our study reports the antidiabetic potential of the isolated flavonoids with predictive pharmacokinetics profile.
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Das T, Ranjan A, Sieroń L, Maniukiewicz W, Das S. Direct Synthesis, Characterization and Theoretical Studies of N‐(6‐Amino‐1,3‐dimethyl‐2,4‐dioxo‐1,2,3,4‐tetrahydropyrimidin‐5‐yl)benzamide Derivatives. ChemistrySelect 2021. [DOI: 10.1002/slct.202004745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tushar Das
- Department of Chemistry National Institute of Technology Patna, Ashok Rajpath Patna 800005 India
- Department of Pharmacoinformatics National Institute of Pharmaceutical Education and Research Hajipur Vaishali Hajipur 844102 India
| | - Amit Ranjan
- Cancer & Translational Research Lab Dr. D.Y. Patil Biotechnology & Bioinformatics Institute Dr. D.Y. Patil Vidyapeeth Pune 411033 India
| | - Lesław Sieroń
- Institute of General and Ecological Chemistry Lodz University of Technology Żeromskiego 116 Łódź Poland
| | - Waldemar Maniukiewicz
- Institute of General and Ecological Chemistry Lodz University of Technology Żeromskiego 116 Łódź Poland
| | - Subrata Das
- Department of Chemistry National Institute of Technology Patna, Ashok Rajpath Patna 800005 India
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Medicinal Chemistry Friendliness of Pigments from Monascus-Fermented Rice and the Molecular Docking Analysis of Their Anti-Hyperlipidemia Properties. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6040111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, the physicochemical properties, pharmacokinetics properties, and drug-likeness of pigments from Monascus-fermented rice (Monascus pigments, MPs) were predicted in silico using SwissADME tool. In silico prediction of physicochemical properties showed that MPs had desirable lipophilic drug-like physicochemical properties including molecular weight (236 to 543), TPSA (44.76 to 179.77), lipophilicity (−0.81 to 4.14), and water solubility (−4.94 to −0.77). The pharmacokinetic properties of MPs (i.e., GIA, P-glycoprotein substrate, and CYP3A4 inhibitor) illustrated that most MPs had high intestinal absorption and bioavailability, but some MPs might cause pharmacokinetics-related drug–drug interactions. Following this, six main well-known MPs (monascin, ankaflavin, rubropunctatin, monascorubrin, rubropunctamine, monascorubramine) were selected for molecular docking with some enzyme receptors. The docking results were shown with the best molecular docking poses, and the interacting residues, number and distance of hydrogen bonds of the MPs and monacolin K (for docking with 3-hydroxy-3-methyl glutaryl coenzyme A reductase (HMG-CoA reductase)), or MPs and oleic acid (for docking with lipase). Dissociation constants showed that MPs had lower inhibitory potential for HMGR (compared with Monacolin K), and higher inhibitory potential for lipase. Individual pigments from Monascus-fermented rice, therefore, have the potential to be developed as drug candidates for controlling hyperlipidemia.
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Abdullahi M, Adeniji SE. In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents. CHEMISTRY AFRICA 2020. [DOI: 10.1007/s42250-020-00162-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractMolecular docking simulation of thirty-five (35) molecules of N-(2-phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamide (IPA) with Mycobacterium tuberculosis target (DNA gyrase) was carried out so as to evaluate their theoretical binding affinities. The chemical structure of the molecules was accurately drawn using ChemDraw Ultra software, then optimized at density functional theory (DFT) using Becke’s three-parameter Lee–Yang–Parr hybrid functional (B3LYP/6-311**) basis set in a vacuum of Spartan 14 software. Subsequently, the docking operation was carried out using PyRx virtual screening software. Molecule 35 (M35) with the highest binding affinity of − 7.2 kcal/mol was selected as the lead molecule for structural modification which led to the development of four (4) newly hypothetical molecules D1, D2, D3 and D4. In addition, the D4 molecule with the highest binding affinity value of − 9.4 kcal/mol formed more H-bond interactions signifying better orientation of the ligand in the binding site compared to M35 and isoniazid standard drug. In-silico ADME and drug-likeness prediction of the molecules showed good pharmacokinetic properties having high gastrointestinal absorption, orally bioavailable, and less toxic. The outcome of the present research strengthens the relevance of these compounds as promising lead candidates for the treatment of multidrug-resistant tuberculosis which could help the medicinal chemists and pharmaceutical professionals in further designing and synthesis of more potent drug candidates. Moreover, the research also encouraged the in vivo and in vitro evaluation study for the proposed designed compounds to validate the computational findings.
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