Article
Biochemistry & Molecular Biology
Navid Jamali, Ehsan Heidari Soureshjani, Gholam-Reza Mobini, Mohammad Samare-Najaf, Cain C. T. Clark, Javad Saffari-Chaleshtori
Summary: This study evaluates medicinal plant compounds as potential inhibitors of the COVID-19 main protease through molecular docking and molecular dynamic analysis, showing that certain phytochemicals have a high tendency to interact with the viral protease and induce conformational changes, potentially leading to enzyme inhibition. Further investigations are needed to explore their medicinal use.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Konda Mani Saravanan, Haiping Zhang, Renganathan Senthil, Kevin Kumar Vijayakumar, Vignesh Sounderrajan, Yanjie Wei, Harshavardhan Shakila
Summary: A novel coronavirus outbreak has posed a severe threat to human healthcare globally, and researchers have been searching for ways to control and prevent this deadly disease. In this study, antiviral compounds from traditional Indian medicinal plants were screened, and amentoflavone was identified as a potential inhibitor of the SARS-CoV2 main protease. Further biochemical experiments are needed to understand the mechanism of inhibition by these plant-derived antiviral compounds.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Vajiheh Eskandari
Summary: This study identified potential repurposing drugs for inhibiting SARS-CoV-2 entry and replication through computational screening. The results showed that bendiamine, folic acid, benfotiamine, and vitamin B12 could bind strongly to the receptor-binding domain of S protein, while bendiamine, folic acid, fursultiamine, and riboflavin were effective against 3CLpro.
JOURNAL OF MOLECULAR MODELING
(2022)
Article
Biology
Alomgir Hossain, Md Ekhtiar Rahman, Md Siddiqur Rahman, Khondokar Nasirujjaman, Mohammad Nurul Matin, Md Omar Faruqe, Muhammad Fazle Rabbee
Summary: Highly transmissive and rapidly evolving COVID-19, caused by SARS-CoV-2, has become a global pandemic and is extensively researched in academia. The main protease (Mpro) of SARS-CoV-2 has been identified as a potential therapeutic target for drug development. A phytochemical library consisting of 2431 compounds from 104 Korean medicinal plants was screened using molecular docking and deep learning, leading to the identification of two lead compounds, Catechin gallate and Quercetin 3-O-malonylglucoside, with inhibitory potency against Mpro.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Multidisciplinary Sciences
Kamonpan Sanachai, Tuanjai Somboon, Patcharin Wilasluck, Peerapon Deetanya, Peter Wolschann, Thierry Langer, Vannajan Sanghiran Lee, Kittikhun Wangkanont, Thanyada Rungrotmongkol, Supot Hannongbua
Summary: This study identified FDA-approved drugs, including lapatinib, as potential inhibitors of the main protease (3CL(pro)) of SARS-CoV-2. The binding behavior of lapatinib with 3CL(pro) was elucidated, and rational design was performed based on the obtained results. The discovery provides an effective repurposed drug and its analogs for inhibiting SARS-CoV-2 3CL(pro).
Article
Biochemistry & Molecular Biology
Suwicha Patnin, Arthit Makarasen, Pongsit Vijitphan, Apisara Baicharoen, Apinya Chaivisuthangkura, Mayuso Kuno, Supanna Techasakul
Summary: In this study, the binding interactions of phenylamino-phenoxy-quinoline derivatives and SARS-CoV-2 main protease (M-pro) were investigated, and two compounds were found to have low binding energy values and appropriate molecular properties for binding to M-pro via hydrogen bonding and Pi-Pi stacking interactions.
Article
Biochemistry & Molecular Biology
Khalid Miandad, Asad Ullah, Kashif Bashir, Saifullah Khan, Syed Ainul Abideen, Bilal Shaker, Metab Alharbi, Abdulrahman Alshammari, Mahwish Ali, Abdul Haleem, Sajjad Ahmad
Summary: This study explored the potential of phytochemicals from Pakistani medicinal plants, particularly Artemisia annua, as inhibitors of the main protease enzyme of SARS-CoV-2. In silico screening and docking techniques were used to assess the binding efficacy of these phytochemicals, with several compounds showing potential as inhibitors. Molecular dynamic simulation analysis and estimation of free binding energies further supported the findings. Experimental validation is needed to confirm the results.
Article
Chemistry, Medicinal
Mohsen Sisakht, Amir Mahmoodzadeh, Maryam Darabian
Summary: A dataset of plant-based natural compounds was screened for antiviral activity against SARS-CoV-2 main protease, with several phytochemicals identified as potential inhibitors that could be used in the fight against COVID-19.
PHYTOTHERAPY RESEARCH
(2021)
Article
Multidisciplinary Sciences
Ala M. Shaqra, Sarah N. Zvornicanin, Qiu Yu J. Huang, Gordon J. Lockbaum, Mark Knapp, Laura Tandeske, David T. Bakan, Julia Flynn, Daniel N. A. Bolon, Stephanie Moquin, Dustin Dovala, Nese Kurt Yilmaz, Celia A. Schiffer
Summary: The study determined the crystal structures of SARS-CoV-2 main protease (Mpro) bound to substrate peptides, defining the substrate envelope and identifying sites susceptible to drug resistance. These findings provide insights for developing robust inhibitors against SARS-CoV-2 and preventing drug resistance.
NATURE COMMUNICATIONS
(2022)
Article
Pharmacology & Pharmacy
Maria Yu. Zakharova, Alexandra A. Kuznetsova, Victoria I. Uvarova, Anastasiia D. Fomina, Liubov I. Kozlovskaya, Elena N. Kaliberda, Inna N. Kurbatskaia, Ivan V. Smirnov, Anatoly A. Bulygin, Vera D. Knorre, Olga S. Fedorova, Alexandre Varnek, Dmitry I. Osolodkin, Aydar A. Ishmukhametov, Alexey M. Egorov, Alexander G. Gabibov, Nikita A. Kuznetsov
Summary: Designing effective target-specific drugs for COVID-19 treatment has become a challenging task for modern science, with M-pro being an attractive target. Studies have identified promising candidate drugs among M-pro inhibitors, and even noncovalent inhibitors can effectively inhibit the enzyme through a fine conformational fit into the active site.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Chemistry, Physical
G. Prateeksha, Tikam S. Rana, Ashish K. Asthana, Brahma N. Singh, Saroj K. Barik
Summary: The study aims to identify potential inhibitors of SARS-CoV-2 through computational evaluation of cryptogamic secondary metabolites. Some metabolites were found to potentially block the virus's major targets, showing promise as inhibitors.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Biochemistry & Molecular Biology
Shama Khan, Zeynab Fakhar, Afzal Hussain, Aijaz Ahmad, Deeba Shamim Jairajpuri, Mohamed F. Alajmi, Md. Imtaiyaz Hassan
Summary: To address the lack of effective drugs or vaccines for COVID-19, researchers used molecular modeling methods to discover potential inhibitors of the SARS-CoV-2 M-pro enzyme. Through simulation studies, they identified five potential inhibitors, one of which showed high affinity and stability in binding to the M-pro. These compounds could be promising candidates for COVID-19 therapy, but further experimental and clinical validation is needed.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biology
Seyed Ali Hemmati, Saeid Tabein
Summary: In this study, researchers used computer-aided methods and insect-derived peptides to develop therapeutic strategies against the main protease of SARS-CoV-2. Through docking and molecular dynamics simulations, they identified two peptides with potential protease inhibitor activities.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Jian Li, Cheng Lin, Xuelan Zhou, Fanglin Zhong, Pei Zeng, Peter J. McCormick, Haihai Jiang, Jin Zhang
Summary: The study found that PF-07304814 developed by Pfizer shows broad-spectrum inhibitory activity against M(pro)s from multiple coronaviruses and provides new insights into the mechanism of inhibition of viral replication through crystal structure analysis. This research may accelerate the development of safer and more effective pan-coronaviral main protease inhibitors.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Venkatramanan Varadharajan, Gokulakrishnan Sivasundari Arumugam, Sethupathi Shanmugam
Summary: This study screened potential SARS-CoV-2 Mpro inhibitors from existing literature on isatin derivatives, ultimately selecting 4 compounds with good ADMET properties and binding energies as lead candidates for further experimental validation and development.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Food Science & Technology
Saikat Mitra, Abu Montakim Tareq, Rajib Das, Talha Bin Emran, Firzan Nainu, Arka Jyoti Chakraborty, Islamudin Ahmad, Trina E. Tallei, Abubakr M. Idris, Jesus Simal-Gandara
Summary: This review discusses the synergistic interactions and specific health benefits of polyphenolic compounds, as well as their bioavailability in humans. The toxicity of some polyphenols is also evaluated. Synergistic treatment approaches using polyphenols may be effective in the treatment of various diseases.
FOOD REVIEWS INTERNATIONAL
(2023)
Article
Chemistry, Organic
Ismail Celik, Gulgun Ayhan-Kilcigil, Berna Guven, Zumra Kara, Arzu Onay-Besikci
Summary: A new class of benzimidazole derivatives was designed and synthesized as potential inhibitors of EGFR tyrosine kinase. In vitro studies showed that compound (6b) with a propyl side chain at the 4th position of triazole rings exhibited 13.8% inhibition. Molecular docking analysis revealed the formation of a hydrogen bond between the most active compound and EGFR. Additionally, predicted ADME profiles indicated favorable pharmacokinetic properties of the synthesized compounds.
POLYCYCLIC AROMATIC COMPOUNDS
(2023)
Article
Biochemistry & Molecular Biology
Jamelah S. Al-Otaibi, Y. Sheena Mary, Shyma Mary, Ravi Trivedi, Brahmananda Chakraborty, Rohitash Yadav, Ismail Celik, Sreejit Soman
Summary: Theoretical analyses of two phenothiazine derivatives were performed using DFT and MD simulations. The study predicted spectroscopic properties and chemical parameters and investigated the stability of protein-ligand complexes formed with these derivatives. The results suggest potential applications of these compounds in interactions with Au and H2O molecules.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Letter
Surgery
Ranjit Sah, Vivek Hada, Aroop Mohanty, Bijaya Padhi, Deepak Chandran, Nawfal R. R. Hussein, Talha B. B. Emran, Wanpen Chaicumpa, Kuldeep Dhama
INTERNATIONAL JOURNAL OF SURGERY
(2023)
Review
Biotechnology & Applied Microbiology
Md. Altamash Ahmad, Harleen Kaur, Pratima Kumari, Ravinder Singh, Rupinder Kaur, Hitesh Chopra, Ojus Sardana, Talha Bin Emran, Kuldeep Dhama
Summary: ChAdOx1 nCoV-19 (AZD1222) is an effective replication-deficient chimpanzee adenovirus vectored vaccine developed by Oxford and AstraZeneca for COVID-19. It has a tolerable safety profile and may prove crucial in boosting herd immunity and relieving the current pandemic.
JOURNAL OF PURE AND APPLIED MICROBIOLOGY
(2023)
Review
Plant Sciences
Gitishree Das, Rajat Nath, Anupam Das Talukdar, Duygu Agagunduz, Birsen Yilmaz, Raffaele Capasso, Han-Seung Shin, Jayanta Kumar Patra
Summary: Java plum, originating from Indonesia and India, is widely recognized for its valuable medicinal properties and is distributed globally in tropical and sub-tropical regions. The plant is rich in various bioactive compounds including alkaloids, flavonoids, terpenes, and tannins. The specific clinical effects and mechanism of action for the major bioactive compounds in Java plum seeds are discussed in this investigation.
Letter
Medicine, General & Internal
Shailesh K. Patel, Jigyasa Rana, Aditya Agrawal, Nikhil K. Channabasappa, Ankush K. Niranjan, Talha B. Emran
ANNALS OF MEDICINE AND SURGERY
(2023)
Article
Biochemistry & Molecular Biology
Shopnil Akash, Md. Mominur Rahman, Clara Mariana Goncalves Lima, Talha Bin Emran, Sharifa Sultana, Sumaira Naz, Tariq Aziz, Metab Alharbi, Abdulrahman Alshammari, Abdullah F. Alasmari
Summary: This study evaluates the dual function of Fisetin and its derivatives against both virus and cancerous targets. Using computational methods and structure-activity relationship analysis, the potential value of these compounds in antitumor and antiviral applications is identified, and molecular docking and ADMET characteristics provide further support for their efficacy.
ACTA BIOCHIMICA POLONICA
(2023)
Article
Chemistry, Medicinal
Trina Ekawati Tallei, Fatimawali, Ahmad Akroman Adam, Dewi Ekatanti, Ismail Celik, Rizka Fatriani, Firzan Nainu, Wisnu Ananta Kusuma, Ali A. Rabaan, Rinaldi Idroes
Summary: This study used multimodal computational studies to uncover the anti-inflammatory properties of fermented pineapple juice. Several compounds were identified that showed potential as anti-inflammatory agents, and molecular docking and dynamics simulations confirmed stable interactions with their respective receptors. These findings provide valuable insights for further experimental validation and development of these compounds as anti-inflammatory agents.
ARCHIV DER PHARMAZIE
(2023)
Article
Chemistry, Applied
Karima Bougueroua, Mokhtaria Yasmina Boufadi, Batoul Latreche, Ismail Celik, Miguel Guerrero Gonzalez, Amina Doubbi Bounoua, Samir Bouras, Ahmed Eissa, Ahmed Zoeir
Summary: This study investigated the effect of UDEE on the treatment of BPH. The results showed that UDEE could significantly reduce prostate enlargement, improve biochemical and histopathological characteristics, and regulate antioxidant activity levels. The safety of UDEE towards the kidney was also demonstrated.
NATURAL PRODUCT RESEARCH
(2023)
Article
Chemistry, Organic
Arpita Paul, James H. H. Zothantluanga, Gourav Rakshit, Ismail Celik, Mithun Rudrapal, Md. Kamaruz Zaman
Summary: This study aimed to identify the phytochemicals responsible for the anti-Alzheimer activity of Morus alba Linn. by targeting proteins such as acetylcholinesterase (AChE) and glycogen synthase kinase-3 beta (GSK-3β). Molecular docking, molecular dynamics simulations, and MM-GBSA calculations were performed, and phytocompounds with code 32, 41, 67, and 70 showed the best activity against AChE and GSK-3β. Based on the computational findings, it was concluded that these phytoconstituents inhibit AChE and GSK-3β, thereby exerting anti-Alzheimer potential.
POLYCYCLIC AROMATIC COMPOUNDS
(2023)
Article
Pharmacology & Pharmacy
Ysrafil Ysrafil, Arlan K. Imran, Prisca Syafriani Wicita, Vyani Kamba, Fihrina Mohamad, Ismail Ismail, Ayyub Harly Nurung, Noviyanty Indjar Gama, Sari Eka Pratiwi, Indwiani Astuti, Firzan Nainu, Talha Bin Emran
Summary: In this study, a mosaic vaccine targeting the mutational spike protein of SARS-CoV-2 was designed using bioinformatics tools. The evaluation of the vaccine showed that it is antigenic, immunogenic, and nonallergenic, with promising physicochemical properties. The vaccine interacts with important receptors by specific amino acid binding, promoting the activation of immune responses. Therefore, this novel designed mosaic vaccine could be a potential candidate for immediate production to combat the COVID-19 pandemic.
Review
Chemistry, Applied
Duygu Agagunduz, Gizem Ozata-Uyar, Betul Kocaadam-Bozkurt, Aycil Ozturan-Sirin, Raffaele Capasso, Saphwan Al -Assaf, Fatih Ozogul
Summary: Food hydrocolloids are versatile natural food ingredients that can be naturally present or added as functional food ingredients or additives. Recent research suggests that certain hydrocolloids can significantly alter the gut microbiota and have positive effects on health. Therefore, investigating the benefits and side effects on the gut may be useful when exploring the health and safety effects of using hydrocolloids as food additives.
FOOD HYDROCOLLOIDS
(2023)
Letter
Medicine, General & Internal
Hitesh Chopra, Muhammad S. Khan, Simona Cavalu, Pradipta R. Rauta, Kuldeep Dhama, Talha B. Emran
ANNALS OF MEDICINE AND SURGERY
(2023)
Letter
Medicine, General & Internal
Talha B. B. Emran, Hitesh Chopra, Kuldeep Dhama
ANNALS OF MEDICINE AND SURGERY
(2023)