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Yakobi S, Zuma L, Pooe O. Investigation into the Interaction between Penicillin-Resistant and Penicillin-Susceptible Gonococcal Penicillin-Binding Protein 2 and Target Phenolic Ligands through Molecular Docking Studies and Structure-Activity Relationship Analysis. Adv Pharmacol Pharm Sci 2024; 2024:2585922. [PMID: 38938595 PMCID: PMC11208787 DOI: 10.1155/2024/2585922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/21/2024] [Accepted: 05/18/2024] [Indexed: 06/29/2024] Open
Abstract
Gonococcal infections present a notable public health issue, and the major approach for treatment involves using β-lactam antibiotics that specifically target penicillin-binding protein 2 (PBP2) in Neisseria gonorrhoeae. This study examines the influence of flavonoids, namely, rutin, on the structural changes of PBP2 in both penicillin-resistant (FA6140) and penicillin-susceptible (FA19) strains. The research starts by clarifying the structural effects of certain mutations, such as the insertion of an aspartate residue at position 345 (Asp-345a), in the PBP2. The strain FA6140, which is resistant to penicillin, shows specific changes that lead to a decrease in penicillin binding. These mutations, namely, P551S and F504L, have a significant impact on the pace at which acylation occurs and the stability of the strain under high temperatures. Molecular docking analyses investigate the antibacterial activities of rutin and other phytocompounds, emphasising rutin's exceptional binding affinity and its potential as an inhibitor of PBP2. Quercetin and protocatechuic acid have encouraging antibacterial effectiveness, with quercetin displaying characteristics similar to those of drugs. Molecular dynamics simulations offer a detailed comprehension of the interactions between flavonoids and PBP2, highlighting rutin's exceptional antioxidant effects and strong affinity for the substrate binding site. The study's wider ramifications pertain to the pressing requirement for antiviral treatments, namely, in the context of the ongoing COVID-19 epidemic. Flavonoids have a strong affinity for binding to PBP2, indicating their potential as inhibitors to impair cell wall formation in N. gonorrhoeae. Ultimately, this study provides extensive knowledge on the interactions between proteins and ligands, the dynamics of the structure, and the ability of flavonoids to combat penicillin-resistant N. gonorrhoeae bacteria. The verified simulation outcomes establish a basis for the creation of potent inhibitors and medicinal therapies to combat infectious illnesses.
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Affiliation(s)
- Sinethemba Yakobi
- School of Life Sciences, Biochemistry, University of KwaZulu-Natal, Durban, South Africa
| | - Lindiwe Zuma
- School of Life Sciences, Biochemistry, University of KwaZulu-Natal, Durban, South Africa
| | - Ofentse Pooe
- School of Life Sciences, Biochemistry, University of KwaZulu-Natal, Durban, South Africa
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2
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Chowdhury R, Bhuia S, Rakib AI, Al Hasan S, Shill MC, El-Nashar HAS, El-Shazly M, Islam MT. Gigantol, a promising natural drug for inflammation: a literature review and computational based study. Nat Prod Res 2024:1-17. [PMID: 38623737 DOI: 10.1080/14786419.2024.2340042] [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: 10/11/2023] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
Gigantol, a bibenzyl compound extracted from various medicinal plants, has shown a number of biological activities, making it an attractive candidate for potential medical applications. This systematic review aims to shed light on gigantol's promising role in inflammation treatment and its underlying mechanisms. Gigantol exhibits potential anti-inflammatory properties in pre-clinical pharmacological test systems. It effectively reduced the levels of pro-inflammatory markers and arachidonic acid metabolites through various pathways, such as NF-κB, AKT, PI3K, and JNK/cPLA2/12-LOX. The in-silico investigations demonstrated that the MMP-13 enzyme served as the most promising target for gigantol with highest binding affinity (docking score = -8.8 kcal/mol). Encouragingly, the absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis of gigantol confirmed its compatibility with the necessary physiochemical, pharmacokinetic, and toxicity properties, bolstering its potential as a drug candidate. Gigantol, with its well-documented anti-inflammatory properties, could be a promising agent for treating inflammation in the near future.
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Affiliation(s)
- Raihan Chowdhury
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
- Bioluster Research Center, Dhaka, Bangladesh
| | - Shimul Bhuia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
- Bioluster Research Center, Dhaka, Bangladesh
| | - Asraful Islam Rakib
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Sakib Al Hasan
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Manik Chandra Shill
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Heba A S El-Nashar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
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3
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Hoseininezhad-Namin MS, Rahimpour E, Jouyban A. Favipiravir, remdesivir, and lopinavir: metabolites, degradation products and their analytical methods. Drug Metab Rev 2024; 56:127-144. [PMID: 38445647 DOI: 10.1080/03602532.2024.2326415] [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: 12/20/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
Severe acute respiratory syndrome 2 (SARS-CoV-2) caused the emergence of the COVID-19 pandemic all over the world. Several studies have suggested that antiviral drugs such as favipiravir (FAV), remdesivir (RDV), and lopinavir (LPV) may potentially prevent the spread of the virus in the host cells and person-to-person transmission. Simultaneously with the widespread use of these drugs, their stability and action mechanism studies have also attracted the attention of many researchers. This review focuses on the action mechanism, metabolites and degradation products of these antiviral drugs (FAV, RDV and LPV) and demonstrates various methods for their quantification and discrimination in the different biological samples. Herein, the instrumental methods for analysis of the main form of drugs or their metabolite and degradation products are classified into two types: optical and chromatography methods which the last one in combination with various detectors provides a powerful method for routine and stability analyses. Some representative studies are reported in this review and the details of them are carefully explained. It is hoped that this review will be a good guideline study and provide a better understanding of these drugs from the aspects investigated in this study.
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Affiliation(s)
- Mir Saleh Hoseininezhad-Namin
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elaheh Rahimpour
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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4
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Chowdhury R, Bhuia MS, Rakib AI, Hasan R, Coutinho HDM, Araújo IM, de Menezes IRA, Islam MT. Assessment of Quercetin Antiemetic Properties: In Vivo and In Silico Investigations on Receptor Binding Affinity and Synergistic Effects. PLANTS (BASEL, SWITZERLAND) 2023; 12:4189. [PMID: 38140516 PMCID: PMC10747098 DOI: 10.3390/plants12244189] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/01/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Quercetin (QUA), a flavonoid compound, is ubiquitously found in plants and has demonstrated a diverse range of biological activities. The primary objective of the current study is to assess the potential antiemetic properties of QUA using an in vivo and in silico approach. In this experiment, 4-day-old chicks were purchased to induce emesis by orally administering copper sulfate pentahydrate (CuSO4·5H2O) at a dose of 50 mg/kg (orally). Domperidone (DOM) (6 mg/kg), Hyoscine (HYS) (21 mg/kg), and Ondansetron (OND) (5 mg/kg) were treated as positive controls (PCs), and distilled water and a trace amount of Tween 80 mixture was employed as a negative control (NC). QUA was given orally at two distinct doses (25 and 50 mg/kg). Additionally, QUA (50 mg/kg) and PCs were administered separately or in combination to assess their antagonistic or synergistic effects on the chicks. The binding affinity of QUA and referral ligands towards the serotonin receptor (5HT3), dopamine receptors (D2 and D3), and muscarinic acetylcholine receptors (M1-M5) were estimated, and ligand-receptor interactions were visualized through various computational tools. In vivo findings indicate that QUA (25 and 50 mg/kg) has a significant effect on reducing the number of retches (16.50 ± 4.65 and 10.00 ± 4.19 times) and increasing the chick latency period (59.25 ± 4.75 and 94.25 ± 4.01 s), respectively. Additionally, QUA (50 mg/kg) in combination with Domperidone and Ondansetron exhibited superior antiemetic effects, reducing the number of retches and increasing the onset of emesis-inducing time. Furthermore, it is worth noting that QUA exhibited the strongest binding affinity against the D2 receptor with a value of -9.7 kcal/mol through the formation of hydrogen and hydrophobic bonds. In summary, the study found that QUA exhibited antiemetic activity in chicks, potentially by interacting with the D2 receptor pathway.
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Affiliation(s)
- Raihan Chowdhury
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.C.); (M.S.B.); (A.I.R.); (R.H.)
| | - Md. Shimul Bhuia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.C.); (M.S.B.); (A.I.R.); (R.H.)
| | - Asraful Islam Rakib
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.C.); (M.S.B.); (A.I.R.); (R.H.)
| | - Rubel Hasan
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.C.); (M.S.B.); (A.I.R.); (R.H.)
| | | | - Isaac Moura Araújo
- Department of Biological Chemistry, Regional University of Cariri—URCA, Crato 63105-000, Brazil; (H.D.M.C.); (I.M.A.)
| | - Irwin Rose Alencar de Menezes
- Department of Biological Chemistry, Regional University of Cariri—URCA, Crato 63105-000, Brazil; (H.D.M.C.); (I.M.A.)
| | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.C.); (M.S.B.); (A.I.R.); (R.H.)
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5
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Khan T, Raza S. Exploration of Computational Aids for Effective Drug Designing and Management of Viral Diseases: A Comprehensive Review. Curr Top Med Chem 2023; 23:1640-1663. [PMID: 36725827 DOI: 10.2174/1568026623666230201144522] [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: 06/21/2022] [Revised: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Microbial diseases, specifically originating from viruses are the major cause of human mortality all over the world. The current COVID-19 pandemic is a case in point, where the dynamics of the viral-human interactions are still not completely understood, making its treatment a case of trial and error. Scientists are struggling to devise a strategy to contain the pandemic for over a year and this brings to light the lack of understanding of how the virus grows and multiplies in the human body. METHODS This paper presents the perspective of the authors on the applicability of computational tools for deep learning and understanding of host-microbe interaction, disease progression and management, drug resistance and immune modulation through in silico methodologies which can aid in effective and selective drug development. The paper has summarized advances in the last five years. The studies published and indexed in leading databases have been included in the review. RESULTS Computational systems biology works on an interface of biology and mathematics and intends to unravel the complex mechanisms between the biological systems and the inter and intra species dynamics using computational tools, and high-throughput technologies developed on algorithms, networks and complex connections to simulate cellular biological processes. CONCLUSION Computational strategies and modelling integrate and prioritize microbial-host interactions and may predict the conditions in which the fine-tuning attenuates. These microbial-host interactions and working mechanisms are important from the aspect of effective drug designing and fine- tuning the therapeutic interventions.
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Affiliation(s)
- Tahmeena Khan
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
| | - Saman Raza
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
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Hasanzadeh Esfahani M, Ghasemi L, Behzad M, Skorepova E, Dusek M. Design, Spectroscopic, and Crystal Structural Characterization of New Pyrazolone-Based Schiff Bases: Molecular Docking Investigations against SARS-Covid-19 Main Proteases (PDB Ids: 6LU7 and 7TLL). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2157026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Liana Ghasemi
- Faculty of Chemistry, Semnan University, Semnan, Iran
| | - Mahdi Behzad
- Faculty of Chemistry, Semnan University, Semnan, Iran
| | - Eliska Skorepova
- Department of Structure Analysis, Institute of Physics ASCR, Prague, Czech Republic
| | - Michal Dusek
- Department of Structure Analysis, Institute of Physics ASCR, Prague, Czech Republic
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7
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Mert-Ozupek N, Calibasi-Kocal G, Olgun N, Basbinar Y, Cavas L, Ellidokuz H. In-silico molecular interactions among the secondary metabolites of Caulerpa spp. and colorectal cancer targets. Front Chem 2022; 10:1046313. [PMID: 36561138 PMCID: PMC9763605 DOI: 10.3389/fchem.2022.1046313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Caulerpa spp. secrete more than thirty different bioactive chemicals which have already been used in cancer treatment research since they play a pivotal role in cancer metabolism. Colorectal cancer is one of the most common cancer types, thus using novel and effective chemicals for colorectal cancer treatment is crucial. In the cheminformatics pipeline of this study, ADME-Tox and drug-likeness tests were performed for filtering the secondary metabolites of Caulerpa spp. The ligands which were selected from the ADME test were used for in silico molecular docking studies against the enzymes of the oxidative branch of the pentose phosphate pathway (glucose-6-phosphate dehydrogenase and 6-phosphoglutarate dehydrogenase), which is of great importance for colorectal cancer, by using AutoDock Vina. Pharmacophore modeling was carried out to align the molecules. Molecular dynamic simulations were performed for each target to validate the molecular docking studies and binding free energies were calculated. According to the ADME test results, 13 different secondary metabolites were selected as potential ligands. Molecular docking studies revealed that vina scores of caulerpin and monomethyl caulerpinate for G6PDH were found as -10.6 kcal mol-1, -10.5 kcal mol-1, respectively. Also, the vina score of caulersin for 6PGD was found as -10.7 kcal mol-1. The highest and the lowest binding free energies were calculated for monomethyl caulerpinate and caulersin, respectively. This in silico study showed that caulerpin, monomethyl caulerpinate, and caulersin could be evaluated as promising marine phytochemicals against pentose phosphate pathway enzymes and further studies are recommended to investigate the detailed activity of these secondary metabolites on these targets.
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Affiliation(s)
- Nazli Mert-Ozupek
- Department of Basic Oncology, Institute of Health Sciences, Dokuz Eylül University, İzmir, Türkiye
| | - Gizem Calibasi-Kocal
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Türkiye
| | - Nur Olgun
- Department of Pediatric Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Türkiye
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Türkiye
| | - Levent Cavas
- Department of Chemistry, Faculty of Sciences, Dokuz Eylül University, İzmir, Türkiye
| | - Hulya Ellidokuz
- Department of Preventive Oncology, Institute of Oncology, Dokuz Eylül University, İzmir, Türkiye,*Correspondence: Hulya Ellidokuz,
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Erol E, Orhan MD, Avsar T, Akdemir A, Okudan ES, Alim Toraman GO, Topcu G. Anti-SARS-CoV-2 and cytotoxic activity of two marine alkaloids from green alga Caulerpa cylindracea Sonder in the Dardanelles. RSC Adv 2022; 12:29983-29990. [PMID: 36321101 PMCID: PMC9580487 DOI: 10.1039/d2ra03358e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022] Open
Abstract
Caulerpa cylindracea Sonder is a green alga belonging to the Caulerpaceae family. This is the first chemical investigation of C. cylindracea in the Dardanelles which resulted in the isolation of four compounds, caulerpin (1), monomethyl caulerpinate (2), beta-sitosterol (3), and palmitic acid (4). Their structures were elucidated by spectroscopic analyses including 1D- and 2D NMR and mass. The isolated compounds 1 and 2 were tested against the SARS-CoV-2 viral targets spike protein and main protease (3CL) enzyme, and both compounds significantly inhibit the interaction of spike protein and ACE2, while the main protease activity was not significantly reduced. Docking studies suggested that compounds 1 and 2 may bind to the ACE2 binding pocket on spike, and compound 2 may also bind to an allosteric site on spike. As such, these compounds may inhibit the spike-ACE2 complex formation competitively and/or allosterically and have the potential to be used against SARS-CoV-2 virus infection. In addition, compounds 1 and 2 showed at least two-fold higher cytotoxicity against breast cancer cell lines MCF7 and MDA-MB-231 compared to the CCD fibroblast control cell line.
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Affiliation(s)
- Ebru Erol
- Dept. of Analytical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University Istanbul Turkey
| | - Muge Didem Orhan
- Bahcesehir University, Health Sciences Institute, Neuroscience Laboratory Istanbul Turkey
| | - Timucin Avsar
- Bahcesehir University, Health Sciences Institute, Neuroscience Laboratory Istanbul Turkey
- Bahcesehir University, School of Medicine, Department of Medical Biology Istanbul Turkey
| | - Atilla Akdemir
- Computer-Aided Drug Discovery Lab., Dept. of Pharmacology, Faculty of Pharmacy, Bezmialem Vakif University Istanbul Turkey
| | - Emine Sukran Okudan
- Faculty of Aquatic Sciences and Fisheries, Akdeniz University Antalya Turkey
| | | | - Gulacti Topcu
- Dept. of Pharmacognosy, Faculty of Pharmacy, Bezmialem Vakif University Istanbul Turkey
- Drug Application & Research Center, Bezmialem Vakif University Istanbul Turkey
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Kalasariya HS, Patel NB, Gacem A, Alsufyani T, Reece LM, Yadav VK, Awwad NS, Ibrahium HA, Ahn Y, Yadav KK, Jeon BH. Marine Alga Ulva fasciata-Derived Molecules for the Potential Treatment of SARS-CoV-2: An In Silico Approach. Mar Drugs 2022; 20:586. [PMID: 36135775 PMCID: PMC9506351 DOI: 10.3390/md20090586] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 12/13/2022] Open
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic. This in silico study aimed to elucidate therapeutic efficacies against SARS-CoV-2 of phyco-compounds from the seaweed, Ulva fasciata. Twelve phyco-compounds were isolated and toxicity was analyzed by VEGA QSAR. Five compounds were found to be nonmutagenic, noncarcinogenic and nontoxic. Moreover, antiviral activity was evaluated by PASS. Binding affinities of five of these therapeutic compounds were predicted to possess probable biological activity. Fifteen SARS-CoV-2 target proteins were analyzed by the AutoDock Vina program for molecular docking binding energy analysis and the 6Y84 protein was determined to possess optimal binding affinities. The Desmond program from Schrödinger's suite was used to study high performance molecular dynamic simulation properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol-6Y84 for better drug evaluation. The ligand with 6Y84 had stronger binding affinities (-5.9 kcal/mol) over two standard drugs, Chloroquine (-5.6 kcal/mol) and Interferon α-2b (-3.8 kcal/mol). Swiss ADME calculated physicochemical/lipophilicity/water solubility/pharmacokinetic properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, showing that this therapeutic agent may be effective against SARS-CoV-2.
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Affiliation(s)
- Haresh S. Kalasariya
- Centre for Natural Products Discovery, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Nikunj B. Patel
- Microbiology Department, Sankalchand Patel University, Visnagar 384315, India
| | - Amel Gacem
- Department of Physics, Faculty of Sciences, University 20 Août 1955, Skikda 21000, Algeria
| | - Taghreed Alsufyani
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Lisa M. Reece
- Reece Life Science Consulting Agency, 819 N Amburn Rd, Texas City, TX 77591, USA
| | - Virendra Kumar Yadav
- Department of Biosciences, School of Liberal Arts & Sciences, Mody University of Science and Technology, Lakshmangarh, Sikar 332311, India
| | - Nasser S. Awwad
- Department of Chemistry, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hala A. Ibrahium
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Semi Pilot Plant, Nuclear Materials Authority, El Maadi, P.O. Box 530, Cairo 11381, Egypt
| | - Yongtae Ahn
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal 462044, India
| | - Byong-Hun Jeon
- Department of Earth Resources & Environmental Engineering, Hanyang University, 222-Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea
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Gupta A, Chauhan SS, Gaur AS, Parthasarathi R. Computational screening for investigating the synergistic regulatory potential of drugs and phytochemicals in combination with 2-deoxy-D-glucose against SARS-CoV-2. Struct Chem 2022; 33:2179-2193. [PMID: 36093277 PMCID: PMC9439941 DOI: 10.1007/s11224-022-02049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/28/2022] [Indexed: 12/15/2022]
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11
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Jahantigh HR, Ahmadi N, Shahbazi B, Lovreglio P, Habibi M, Stufano A, Gouklani H, Ahmadi K. Evaluation of the dual effects of antiviral drugs on SARS-CoV-2 receptors and the ACE2 receptor using structure-based virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 2022:1-23. [DOI: 10.1080/07391102.2022.2103735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Hamid Reza Jahantigh
- Interdisciplinary Department of Medicine - Section of Occupational Medicine, University of Bari, Bari, Italy
- Animal Health and Zoonosis PhD Course, Department of Veterinary Medicine, University of Bari, Bari, Italy
| | - Nahid Ahmadi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behzad Shahbazi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Piero Lovreglio
- Interdisciplinary Department of Medicine - Section of Occupational Medicine, University of Bari, Bari, Italy
| | - Mehri Habibi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran
| | - Angela Stufano
- Interdisciplinary Department of Medicine - Section of Occupational Medicine, University of Bari, Bari, Italy
- Animal Health and Zoonosis PhD Course, Department of Veterinary Medicine, University of Bari, Bari, Italy
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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12
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Zheng Z, Deng H, Cai Z, Liao X, Xu S. Synthesis of the Octameric Ring Containing Compound Caulerpin Using a Knoevenagel Reaction Catalyzed by an Amino Acid ‐ Ionic Liquid Solvent. ChemistrySelect 2022. [DOI: 10.1002/slct.202201381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zhang‐Fan Zheng
- Department of Chemistry College of Chemistry and Materials Science Jinan University Guangzhou 510632 P. R. China
| | - Hong Deng
- Department of Chemistry College of Chemistry and Materials Science Jinan University Guangzhou 510632 P. R. China
| | - Zi‐Jie Cai
- Department of Chemistry College of Chemistry and Materials Science Jinan University Guangzhou 510632 P. R. China
| | - Xiao‐Jian Liao
- Department of Chemistry College of Chemistry and Materials Science Jinan University Guangzhou 510632 P. R. China
| | - Shi‐Hai Xu
- Department of Chemistry College of Chemistry and Materials Science Jinan University Guangzhou 510632 P. R. China
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Üstün E, Düşünceli SD, Coşkun F, Özdemir İ. Molybdenum Carbonyl Complexes with Benzimidazole Derivatives Against SARS-CoV-2 by Molecular Docking and DFT/TDDFT Methods. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Benzimidazole derivative molecules attract attention of scientists due to their bioactivities. The dramatic changes in recorded activities according to the type and position of the substituents motivate synthesis and analysis of new molecules. Commercial benzimidazole-based molecules have been used in therapeutic procedures. It is known that the activities of metal complexes with benzimidazole derivative ligands have different activities when compared to the benzimidazole main structure. Nowadays, one of the most important health problems is COVID-19, which caused the pandemic that we are still experiencing. Although vaccine studies are important to overcome acute problems, regarding the possible post-vaccination adverse effects, the need for new drugs against the virus is obvious. Considering the urgency and the limited facilities during the pandemic, preliminary in silico studies of candidate molecules are essential. In this study, {[bis-(N-benzylbenzimidazole)] tetracarbonylmolybdenum}, {[bis-(N-4-chlorobenzylbenzimidazole)] tetracarbonylmolybdenum} and {[bis-(N-4-methoxybenzylbenzimidazole)] tetracarbonylmolybdenum} were synthesized and characterized. The optimization and the structural analysis of these molecules were performed by DFT/TDDFT methods. The molecules were docked into SARS coronavirus main peptidase (PDB ID: 2gtb), COVID-19 main protease in complex with Z219104216 (PDB ID: 5r82), COVID-19 main protease in complex with an inhibitor N3 (PDB ID: 6lu7) and Papain-like protease of SARS-CoV-2 (PDB ID: 6w9c) crystal structures for evaluation of their anti-viral activity.
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Affiliation(s)
- Elvan Üstün
- Department of Chemistry, Faculty of Art and Science, Ordu University, 52200 Ordu, Turkey
| | - Serpil Demir Düşünceli
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| | - Feyzullah Coşkun
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| | - İsmail Özdemir
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
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Kumar V, Parate S, Yoon S, Lee G, Lee KW. Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2. Front Microbiol 2021; 12:647295. [PMID: 33967984 PMCID: PMC8097174 DOI: 10.3389/fmicb.2021.647295] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/25/2021] [Indexed: 01/18/2023] Open
Abstract
The rapid spread of COVID-19, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a worldwide health emergency. Unfortunately, to date, a very small number of remedies have been to be found effective against SARS-CoV-2 infection. Therefore, further research is required to achieve a lasting solution against this deadly disease. Repurposing available drugs and evaluating natural product inhibitors against target proteins of SARS-CoV-2 could be an effective approach to accelerate drug discovery and development. With this strategy in mind, we derived Marine Natural Products (MNP)-based drug-like small molecules and evaluated them against three major target proteins of the SARS-CoV-2 virus replication cycle. A drug-like database from MNP library was generated using Lipinski's rule of five and ADMET descriptors. A total of 2,033 compounds were obtained and were subsequently subjected to molecular docking with 3CLpro, PLpro, and RdRp. The docking analyses revealed that a total of 14 compounds displayed better docking scores than the reference compounds and have significant molecular interactions with the active site residues of SARS-CoV-2 virus targeted proteins. Furthermore, the stability of docking-derived complexes was analyzed using molecular dynamics simulations and binding free energy calculations. The analyses revealed two hit compounds against each targeted protein displaying stable behavior, binding affinity, and molecular interactions. Our investigation identified two hit compounds against each targeted proteins displaying stable behavior, higher binding affinity and key residual molecular interactions, with good in silico pharmacokinetic properties, therefore can be considered for further in vitro studies.
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Affiliation(s)
- Vikas Kumar
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| | - Shraddha Parate
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju, South Korea
| | - Sanghwa Yoon
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| | - Gihwan Lee
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU), Jinju, South Korea
| | - Keun Woo Lee
- Division of Life Sciences, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
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