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Field-Template, QSAR, Ensemble Molecular Docking, and 3D-RISM Solvation Studies Expose Potential of FDA-Approved Marine Drugs as SARS-CoVID-2 Main Protease Inhibitors

Poonam Kalhotra, Veera C.S.R. Chittepu, Guillermo Osorio-Revilla, Tzayhri Gallardo-Velazquez
2021 Molecules  
Initially, field-template and structureactivity atlas models were constructed to understand and explain the molecular features responsible for SARS-CoVID-2 main protease inhibitors, which revealed that  ...  SARS-CoVID-2 main protease is one of the therapeutic drug targets that has been shown to reduce virus replication, and its high-resolution 3D structures in complex with inhibitors have been solved.  ...  further optimize their efficiency and potency, and to help in identifying new natural inhibitors of SARS=CoVID-19 main-protease enzyme, the structure-activity relationship (S.A.R.) was studied using the  ... 
doi:10.3390/molecules26040936 pmid:33578831 pmcid:PMC7916619 fatcat:wv5ze3o6cfdsfb2til7yifvr2i

Evaluation of inhibitory effects of benzothiazole and 3-amino-benzothiazolium derivatives on DNA topoisomerase II by molecular modeling studies

E. Aki-Yalcin, T. Ertan-Bolelli, T. Taskin-Tok, O. Ozturk, S. Ataei, C. Ozen, I. Yildiz, I. Yalcin
2014 SAR and QSAR in environmental research (Print)  
In this study the interactions between DNA topoisomerase II and the compounds were examined in detail by molecular modelling studies such as molecular docking and pharmacophore analysis performed using  ...  As a result, it was found that benzothiazolium compounds exhibited a totally different mechanism than benzothiazoles by binding to the different amino acids at the active site of the protein molecule.  ...  In the drug design area, quantitative structure-activity relationship (QSAR) method is an area of research pioneered by Hansch and Leo [25] and Hansch and Fujita [26] .  ... 
doi:10.1080/1062936x.2014.923039 pmid:25027467 fatcat:g3vov6mstnfrla3h7zqfucuhvm

A Biophysical Approach to SARS-CoV-2 Pathogenicity

Claudio Messori
2021 OALib  
and solving the intracel- lular crowding and molecular self-assembly problems by way of chirality (handedness of molecules) and magnetization  ...  This enhanced structural feature can be correlated with higher channelling activity in SARS-CoV-2 than in SARS-CoV-1.  ... 
doi:10.4236/oalib.1108183 fatcat:k3lqk453g5gglooqbotatitege

Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: lessons from the pandemic and preparing for future health crises

Natesh Singh, Bruno O Villoutreix
2021 Computational and Structural Biotechnology Journal  
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients.  ...  In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides.  ...  Acknowledgements Declaration of Competing Interest References Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that  ... 
doi:10.1016/j.csbj.2021.04.059 pmid:33936562 pmcid:PMC8074526 fatcat:brqnldsbkvftlhbre4ax63dcfq

In silicomodels for predicting vector control chemicals targetingAedes aegypti

J. Devillers, C. Lagneau, A. Lattes, J.C. Garrigues, M.M. Clémenté, A. Yébakima
2014 SAR and QSAR in environmental research (Print)  
Fortunately, the use of quantitative structure-activity relationship (QSAR) modelling allows the reduction of time and cost in the discovery of new chemical structures potentially active against mosquitoes  ...  This is because the high cost of the discovery of an insecticide is not counterbalanced by the 'low profitability' of the vector control market.  ...  The structures of several Cry toxins, including Cry4Aa [76] and Cry4Ba [77] , have been solved by X-ray crystallography.  ... 
doi:10.1080/1062936x.2014.958291 pmid:25275884 pmcid:PMC4200584 fatcat:i3hp4mr5pvhzxfdgetyypwgu2a

A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets

Giulia Russo, Valentina Di Salvatore, Giuseppe Sgroi, Giuseppe Alessandro Parasiliti Palumbo, Pedro A Reche, Francesco Pappalardo
2021 Briefings in Bioinformatics  
As a working example, we applied this problem solving protocol to predict the cross-reactivity of pre-existing vaccination interventions against SARS-CoV-2.  ...  The COVID-19 pandemic has highlighted the need to come out with quick interventional solutions that can now be obtained through the application of different bioinformatics software to actively improve  ...  Publication costs are covered by STriTuVaD project.  ... 
doi:10.1093/bib/bbab403 pmid:34607353 pmcid:PMC8500048 fatcat:2hgst7w32vepfl2xcqobfhaihe

Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies

Mohammad Moni, Pietro Liò
2014 BMC Bioinformatics  
By using neighbourhood based benchmark and topological methods, we have built comorbidity relationships network based on the OMIM and our identified significant genes.  ...  The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number  ...  Our results indicate that such a combination of molecular and population-level data could help to build novel hypotheses about disease mechanisms.  ... 
doi:10.1186/1471-2105-15-333 pmid:25344230 pmcid:PMC4363349 fatcat:5mnvbhkfgffwjohuurq25jbfr4

ACE2 polymorphisms and individual susceptibility to SARS-CoV-2 infection: insights from an in silico study [article]

Matteo Calcagnile, Patricia Forgez, Antonio Iannelli, Cecilia Bucci, Marco Alifano, Pietro Alifano
2020 bioRxiv   pre-print
The current SARS covid-19 epidemic spread appears to be influenced by ethnical, geographical and sex-related factors that may involve genetic susceptibility to diseases.  ...  Similar to SARS-CoV, SARS-CoV-2 exploits angiotensin-converting enzyme 2 (ACE2) as a receptor to invade cells, notably type II alveolar epithelial cells. Importantly, ACE2 gene is highly polymorphic.  ...  As 6VW1 was generated with a chimeric SARS-CoV/SARS-CoV-2 Spike, to support our results we performed an additional simulation by challenging the ACE2 structure from 6VW1 with the Spike structures that  ... 
doi:10.1101/2020.04.23.057042 fatcat:w47aq2744nelvai2pbcxgriu2u

Phage-Displayed Mimotopes of SARS-CoV-2 Spike Protein Targeted to Authentic and Alternative Cellular Receptors

Valery A. Petrenko, James W. Gillespie, Laura Maria De Plano, Michael A. Shokhen
2022 Viruses  
Phage mimotopes of the SARS-CoV-2 Spike S1 protein have been developed using a combination of phage display and molecular mimicry concepts, termed here "phage mimicry", supported by bioinformatics methods  ...  The evolution of the SARS-CoV-2 virus during the COVID-19 pandemic was accompanied by the emergence of new heavily mutated viral variants with increased infectivity and/or resistance to detection by the  ...  Acknowledgments: Anticancer cell-targeted landscape phages used in this project have been developed by students and members of the Petrenko laboratory: Bedi, D., De Plano, L.M., Fagbohun, O.A., Gross,  ... 
doi:10.3390/v14020384 pmid:35215976 pmcid:PMC8879608 fatcat:xwywd7egvrflnnuekfdwhau3zu

The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors

Lucia Silvestrini, Norhan Belhaj, Lucia Comez, Yuri Gerelli, Antonino Lauria, Valeria Libera, Paolo Mariani, Paola Marzullo, Maria Grazia Ortore, Antonio Palumbo Piccionello, Caterina Petrillo, Lucrezia Savini (+2 others)
2021 Scientific Reports  
We find that these inhibitors affect dimerization and enzymatic activity to a different extent and sometimes in an opposite way, likely due to the different molecular mechanisms underlying the two processes  ...  The Mpro residues that emerge as key to optimize both dissociation and enzymatic activity inhibition are discussed.  ...  On these grounds, the experimental results obtained in the present study, together with the structure of the seven inhibitors within the M pro active site determined by the refined molecular docking, can  ... 
doi:10.1038/s41598-021-88630-9 pmid:33927258 fatcat:rinuguhfojcobgyxjm6cy5cbxy

Origin of SARS-CoV-2: Two Schools of Thought

Sehgal ML
2021 Biomedical Journal of Scientific & Technical Research  
ARTICLE INFO ABSTRACT Undisputedly, the horseshoe bats are the nearest known genetic relatives of the Sars-CoV-2 virus.  ...  However, most intriguing question is to explain how did a bat RNA virus evolve into a human pathogen and became so virulent and deadly unlike its predecessors of the likes Sars-Co V (  ...  those shown in SARS-CoV to be optimal for receptor binding [23, 30] .  ... 
doi:10.26717/bjstr.2021.37.005989 fatcat:3i37ijp3zvdjlgt2hq27x26nsy

Mixing Pharmacophore Modeling and Classical QSAR Analysis as Powerful Tool for Lead Discovery [chapter]

Mutasem O.
2012 Virtual Screening  
This problem can be very significant in cases of large SAR lists.  ...  We found that the best way to solve this problem is by exploring the pharmacophoric space of several carefully selected training Mixing Pharmacophore Modeling and Classical QSAR Analysis  ... 
doi:10.5772/20993 fatcat:kqsoyxazincp3eesgflyqejpdm

SARS-CoV-2 will constantly sweep its tracks: a vaccine containing CpG motifs in 'lasso' for the multi-faced virus

V. V. Oberemok, K. V. Laikova, K. A. Yurchenko, N. A. Marochkin, I. I. Fomochkina, A. V. Kubyshkin
2020 Inflammation Research  
We found that CpG dinucleotides are the least rare dinucleotides in the genomes of SARS-CoV-2 and other known human coronaviruses, and hypothesized that their higher frequency could be responsible for  ...  the unwanted increased lethality to the host, causing a 'cytokine storm' in people who overexpress cytokines through the activation of specific Toll-like receptors in a manner similar to TLR9-CpG ODN interactions  ...  Acknowledgements This work was supported by state program No FZEG-2020-0060 of the Ministry of Science and Higher Education of Russian Federation.  ... 
doi:10.1007/s00011-020-01377-3 pmid:32656668 pmcid:PMC7354743 fatcat:pwa6otatnzck7olbpt2k2c6h2q

Review: Development of SARS-CoV-2 immuno-enhanced COVID-19 vaccines with nano-platform

Nawamin Sa-nguanmoo, Katawut Namdee, Mattaka Khongkow, Uracha Ruktanonchai, YongXiang Zhao, Xing-Jie Liang
2021 Nano Reseach  
The discussion about their safe, effective, and affordable vaccines to immunize against COVID-19 will be highlighted.  ...  This is due to the fact that nano-based vaccines are stable, able to target, form images, and offer an opportunity to enhance the immune responses.  ...  The idea of protein engineering has started since 1980s with the purposes to synthesize enzymes, redesign antibodies, analyze molecular recognition, and determine structure-activity relationships [334  ... 
doi:10.1007/s12274-021-3832-y pmid:34659650 pmcid:PMC8501370 fatcat:gmyauiuzpfgujnkfyeppsjbkiy

Evaluation of the Tubulin-Bound Paclitaxel Conformation: Synthesis, Biology, and SAR Studies of C-4 to C-3' Bridged Paclitaxel Analogues

Thota Ganesh, Chao Yang, Andrew Norris, Tom Glass, Susan Bane, Rudravajhala Ravindra, Abhijit Banerjee, Belhu Metaferia, Shala L. Thomas, Paraskevi Giannakakou, Ana A. Alcaraz, Ami S. Lakdawala (+2 others)
2007 Journal of Medicinal Chemistry  
Having optimized the macrocyclic bridge between the C-4 acyl and the C-3′ o-phenyl positions, we next investigated the structure-activity relationships at other sites of the bridged paclitaxel analogues  ...  The groundbreaking work of Nogales, Wolf, and Downing that solved the structure of R -tubulin by electron crystallography (EC) was made possible, in part, by stabilizing sheets of polymerized tubulin with  ... 
doi:10.1021/jm061071x pmid:17263521 pmcid:PMC2585518 fatcat:6sbm76e2zjddndksigufwrceou
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