In-silico and in-vitro functional validation of imidazole derivatives as potential sirtuin inhibitor by Uma Maheswara Rao Dindi, Suhadha Parveen Sadiq, Sameer Al-Ghamdi, Naif Abdurhman Alrudian, Salman Bin Dayel, Abdulwahab Ali Abuderman, Mohammad Shahid, Thiyagarajan Ramesh, Ravikumar Vilwanathan

“…RT-PCR and Western blot analyses were performed to understand the impact of ligands on the gene and protein expression of Class III HDAC enzymes.Results and discussionWe evaluated the sirtuin inhibition activity of our in-house compound comprised of imidazole derivatives by docking the molecules with the protein data bank. ADME properties of all the compounds used in the study were evaluated, and it was found that all fall within the favorable range of being a potential drug. …”
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Relevance of <i>ARID1A</i> Mutations in Endometrial Carcinomas by Antonio De Leo, Gloria Ravegnini, Francesco Musiani, Thais Maloberti, Michela Visani, Viviana Sanza, Sabrina Angelini, Anna Myriam Perrone, Pierandrea De Iaco, Angelo Gianluca Corradini, Francesca Rosini, Marco Grillini, Donatella Santini, Claudio Ceccarelli, Claudio Zamagni, Giovanni Tallini, Dario de Biase

“…Moreover, we have investigated if <i>ARID1A</i> mutations may alter the protein structure, using the Protein Data Bank sequence. We found a good correlation between <i>ARID1A</i> mutations and protein immunostaining, even if we did not find statistically significant differences in the <i>ARID1A</i> expression levels. …”
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Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm by Pedro M. Martins, Lucianna H. Santos, Diego Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de S. Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina A. Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira, Raquel C. de Melo-Minardi

“…Propedia comprises over 19,000 high-resolution structures from the Protein Data Bank including structural and sequence information from protein–peptide complexes. …”
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Bioinformatics and immunoinformatics assisted multiepitope vaccine construct against Burkholderia anthina by Maha A. Alshiekheid, Ali M. Dou, Mohammad Algahtani, Wafa Abdullah I. Al-Megrin, Yaseer Ali Alhawday, Arwa Essa Alradhi, Khulud Bukhari, Basmah F. Alharbi, Ahmed N. Algefary, Basmah Awwadh Alhunayhani, Khaled S. Allemailem

“…The vaccine construct was designed by joining selected epitopes with the help of a GPGPG linker and additionally linked with cholera toxin b subunit adjuvant to increase the efficacy of the vaccine construct the sequence of the said adjuvant were retrieved from protein data bank through its (PDB ID: 5ELD). The designed vaccine construct was evaluated for its physiochemical properties analysis in which we reported that the vaccine construct comprises 216 amino acids with a molecular weight of 22.37499 kilo Dalton, 15.55 instability index (II) is computed, and this classifies that the vaccine construct is properly stable. …”
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Unsymmetrical aromatic disulfides as SARS-CoV-2 Mpro inhibitors: Molecular docking, molecular dynamics, and ADME scoring investigations by Samir Chtita, Salah Belaidi, Faizan Abul Qais, Mebarka Ouassaf, Muneerah Mogren AlMogren, Ateyah A. Al-Zahrani, Mohamed Bakhouch, Assia Belhassan, Hanane Zaki, Mohammed Bouachrine, Tahar Lakhlifi

“…The optimal binding features of disulfides within the binding pocket of SARS-CoV-2 endoribonuclease protein (Protein Data Bank [PDB]: 6LU7) was described. Studied compounds were ranked for potential effectiveness, and those have shown high molecular docking scores were proposed as novel drug candidates against SARS-CoV-2. …”
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Assessing the therapeutic potential of agomelatine, ramelteon, and melatonin against SARS-CoV-2 by Pradeep Kumar Yadalam, Thodur Madapusi Balaji, Saranya Varadarajan, Khalid J. Alzahrani, Mohammad S. Al-Ghamdi, Hosam Ali Baeshen, Mohammed Farhan A. Alfarhan, Zohaib Khurshid, Shilpa Bhandi, Raghunathan Jagannathan, Vikrant R. Patil, A. Thirumal Raj, Jithendra Ratnayake, Shankargouda Patil

“…For facilitation of readability by the AutoDock software conversion to PDBQT(Protein Data Bank, Partial Charge (Q), &amp; Atom Type (T)) format was performed. …”
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Observation of an E2 (Ubc9)-homodimer by crystallography by Aileen Y. Alontaga, Nigus D. Ambaye, Yi-Jia Li, Ramir Vega, Chih-Hong Chen, Krzysztof P. Bzymek, John C. Williams, Weidong Hu, Yuan Chen

“…The data of the crystal structure has been deposited to RCSB protein data bank with identifier: 4Y1L. Keywords: SUMO, Poly-SUMO chain, RWD, Ubiquitin, Ubc9, E1, Ubiquitin-like, Modifications…”
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Virtual Screening of <i>Artemisia annua</i> Phytochemicals as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme by Khalid Miandad, Asad Ullah, Kashif Bashir, Saifullah Khan, Syed Ainul Abideen, Bilal Shaker, Metab Alharbi, Abdulrahman Alshammari, Mahwish Ali, Abdul Haleem, Sajjad Ahmad

“…The X-ray crystal structure of the main protease of SARS-CoV-2 with an <b>N3</b> inhibitor was obtained from the protein data bank while <i>A. annua</i> phytochemicals were retrieved from different drug databases. …”
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Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein by Noah Giacon, Ettore Lo Cascio, Darcy S. Davidson, Marcelo D. Polêto, Justin A. Lemkul, Valeria Pennacchietti, Livia Pagano, Carlotta Zamparelli, Angelo Toto, Alessandro Arcovito

“…Moreover, we present a detailed computational analysis of the complex between the C-terminal portion of E protein with ZO1-PDZ2, both in its monomeric conformation (computed as a high confidence AlphaFold2 model) and dimeric conformation (obtained from the Protein Data Bank), by using both polarizable and nonpolarizable simulations. …”
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In silico and in vivo screening of triamterene synthetic analogues as promising diuretics by K.V. Sokolova, V.V. Stavytskyi, O.Yu. Voskoboinik, O.A. Podpletnya, S.I. Kovalenko

“…Macromolecular data were downloaded from the Protein Data Bank (PDB) namely, the crystal structures of epithelial sodium channel (ENaC) ((PDB ID – 6WTH). …”
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Optimization Rules for SARS-CoV-2 M^pro Antivirals: Ensemble Docking and Exploration of the Coronavirus Protease Active Site by Shana V. Stoddard, Serena D. Stoddard, Benjamin K. Oelkers, Kennedi Fitts, Kellen Whalum, Kaylah Whalum, Alexander D. Hemphill, Jithin Manikonda, Linda Michelle Martinez, Elizabeth G. Riley, Caroline M. Roof, Nowreen Sarwar, Doni M. Thomas, Emily Ulmer, Felissa E. Wallace, Pankaj Pandey, Sudeshna Roy

“…The results of molecular dynamic (MD) simulation of cinanserin-optimized compounds CM02, CM06, and CM07 revealed that CM02 and CM06 fit well into the active site of SARS-CoV-2 M^pro [Protein Data Bank (PDB) accession number 6LU7] and formed strong and stable interactions with the key residues, Ser-144, His-163, and Glu-166. …”
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Structure-Aware Mycobacterium tuberculosis Functional Annotation Uncloaks Resistance, Metabolic, and Virulence Genes by Samuel J. Modlin, Afif Elghraoui, Deepika Gunasekaran, Alyssa M. Zlotnicki, Nicholas A. Dillon, Nermeeta Dhillon, Norman Kuo, Cassidy Robinhold, Carmela K. Chan, Anthony D. Baughn, Faramarz Valafar

“…Second, we modeled 1,711 underannotated proteins and developed a semiautomated pipeline that captured shared function between 400 protein models and structural matches of known function on Protein Data Bank, including drug efflux proteins, metabolic enzymes, and virulence factors. …”
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FDA-Approved Drugs with Potent In Vitro Antiviral Activity against Severe Acute Respiratory Syndrome Coronavirus 2 by Ahmed Mostafa, Ahmed Kandeil, Yaseen A. M. M. Elshaier, Omnia Kutkat, Yassmin Moatasim, Adel A. Rashad, Mahmoud Shehata, Mokhtar R. Gomaa, Noura Mahrous, Sara H. Mahmoud, Mohamed GabAllah, Hisham Abbas, Ahmed El Taweel, Ahmed E. Kayed, Mina Nabil Kamel, Mohamed El Sayes, Dina B. Mahmoud, Rabeh El-Shesheny, Ghazi Kayali, Mohamed A. Ali

“…A virtual screening study illustrated that Azithromycin, Niclosamide, and Nitazoxanide bind to the main protease of SARS-CoV-2 (Protein data bank (PDB) ID: 6lu7) in binding mode similar to the reported co-crystalized ligand. …”
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Reverse Screening Methods to Search for the Protein Targets of Chemopreventive Compounds by Hongbin Huang, Hongbin Huang, Guigui Zhang, Guigui Zhang, Yuquan Zhou, Yuquan Zhou, Chenru Lin, Chenru Lin, Suling Chen, Suling Chen, Yutong Lin, Yutong Lin, Shangkang Mai, Shangkang Mai, Zunnan Huang, Zunnan Huang

“…Several large software packages, such as Schrödinger and Discovery Studio; typical software/network services such as ChemMapper, PharmMapper, idTarget, and INVDOCK; and practical databases of known target ligands and receptor crystal structures, such as ChEMBL, BindingDB, and the Protein Data Bank (PDB), are available for use in these computational methods. …”
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In-silico analysis of the inhibition of the SARS-CoV-2 main protease by some active compounds from selected African plants by Haruna I. Umar, HND, Sunday S. Josiah, MTech, Tolulope P. Saliu, MSc, Tajudeen O. Jimoh, MTech, Adeola Ajayi, BSc, Jamilu B. Danjuma, PGD

“…Methods: The crystal structure of Mpro was retrieved from the Protein Data Bank, while the plant bioactive compounds were retrieved from Pubchem. …”
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Structural studies of the RPFF protein involved in Quorum Sensing and the IGHMBP2 protein involved in Spinal Muscular Atrophy with Respiratory Distress type 1 by Lim, Siew Choo

“…Structural homology search in the Protein Data Bank revealed that RpfF is structurally similar to members of the hydratase/ isomerase superfamily. …”
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Anti-breast cancer effect and molecular mechanism of action of artonin e using In Silico, In Vitro and In Vivo approaches by Etti, Imaobong Christopher

“…The structure of the ligand binding domain of hERα was retrieved from Protein Data Bank while the structures of compounds were collected from PubChem database and prepared with the Schrodinger Suite. …”
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Design and search for prospective diuretics (CA II Inhibitors) among aroylhydrazones of esters quinone oxime using in silico and in vivo methodology by K.V. Sokolova, V.V. Stavytskyi, S.О. Konovalova, O.A. Podpletnya, S.I. Kovalenko, A.P. Avdeenko

“…Macromolecular data of the crystal structure of CA II (PDB ID – 3HS4) were downloaded from the Protein Data Bank (PDB). The design was developed and the search for diuretic agents among benzohydrazides of O-aroyl esters of quinone oximes was developed using in silico methods (prediction of affinity, lipophilicity, toxicity and enzyme-ligand interactions), traditional organic synthesis, and in vivo methods (effect on excretory function of rat kidneys). …”
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Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K by David R. Lisgarten, Rex A. Palmer, Carina M. C. Lobley, Claire E. Naylor, Babur Z. Chowdhry, Zakieh I. Al-Kurdi, Adnan A. Badwan, Brendan J. Howlin, Nicholas C. J. Gibbons, José W. Saldanha, John N. Lisgarten, Ajit K. Basak

“…The crystal structure, also at 0.92 Å and 100 K, of a second commercially available form of human recombinant insulin, Intergen (II), deposited in the Protein Data Bank as 3W7Y which remains otherwise unpublished is compared here with the Insugen (I) structure. …”
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A Study on the Anti-NF-κB, Anti-<i>Candida</i>, and Antioxidant Activities of Two Natural Plant Hormones: Gibberellin A4 and A7 by Bruno Dias Nani, Pedro Luiz Rosalen, Josy Goldoni Lazarini, Janaína de Cássia Orlandi Sardi, Diego Romário-Silva, Leonardo Pereira de Araújo, Mateus Silva Beker dos Reis, Isadora Breseghello, Thiago Mattar Cunha, Severino Matias de Alencar, Nelson José Freitas da Silveira, Marcelo Franchin

“…GA4 in silico anti-NF-κB activity was evaluated by molecular docking with the software “AutoDock Vina”, “MGLTools”, “Pymol”, and “LigPlot+”, based on data obtained from “The Uniprot database”, “Protein Data Bank”, and “PubChem database”. The GA4 and GA7 in vitro anti-<i>Candida</i> effects against <i>Candida albicans</i> (MYA 2876) were determined (MIC and MFC). …”
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