RSC Advances Blog

We are very pleased to introduce Professor Hamdy M. Abdel-Rahman, Dr Asmaa M. AboulMagd and Mr Mostafa A. Mansour, the authors of the paper ‘Quinazoline-Schiff base conjugates: in silico study and ADMET predictions as multi-target inhibitors of coronavirus (SARS-CoV-2) proteins‘. Their article has been very well received and handpicked by our reviewers and handling editors as one of our September HOT articles. The authors told us more about the work that went into this article and what they hope to achieve in the future. You can find out more about the authors and their article below and find more HOT articles in our online collection.

Meet the authors

Prof. Hamdy M. Abdel-Rahman received the Ph.D. degree in medicinal chemistry in 1999 in a joint supervision system between Faculty of Pharmacy Assiut University, Egypt and Kyoto Pharmaceutical University, Japan. After Two postdoctoral positions, from 2002-2004, at Kyoto Pharmaceutical University, Japan and from 2006-2009 at institute of cancer therapeutics, Bradford University, UK; he returned back to Assiut University, Egypt where he promoted to full professor in 2012. From 2014 he joined the Faculty of Pharmacy, Nahda University, Egypt, where he is the dean from 2018 till now.

Dr. Asmaa M. AboulMagd received the Ph.D. degree in pharmaceutical chemistry in 2016 from Faculty of Pharmacy, Ain Shams University. She is interested in design and synthesis of small molecules with potential biological activities and the use of computer aided drug design. Since 2017, she has been a lecturer of pharmaceutical chemistry at Faculty of Pharmacy, Nahda University, Egypt, till now.

Mr. Mostafa A. Mansour graduated from Faculty of pharmacy, Nahda University, Egypt in 2013 and received the Master degree in medicinal chemistry in 2020 from Faculty of Pharmacy, Beni-Suef University, Egypt. Interested in computer aided drug design techniques.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
The focus of this article is to find a drug for treatment of coronavirus diseases COVID-19.

How big an impact could your results potentially have?
Reaching to a therapeutic drug against coronavirus will have a social, economic, and political impact.

Could you explain the motivation behind this study?
In a previous work, we have designed and synthesized a class of synthetic compounds and were evaluated against PDE 4B activity (anti-inflammatory in chest diseases), we thought that this would be ideal pharmaceutical therapy against COVID-19 disease.

In your opinion, what are the key design considerations for your study?
The key design considerations in this study is to find out that these compounds could be used as potential therapeutic agents for COVID-19.

Which part of the work towards this paper proved to be most challenging?
COVID-19 pandemic is considered as a global health crisis of our time and the greatest challenge we have faced nowadays.

What aspect of your work are you most excited about at the moment?
Using computer modeling softwares, we proved that these compounds have a potential therapeutic effect on coronavirus by several mechanisms.

What is the next step? What work is planned?
The in-vitro evaluation of the biological activity of the synthesized derivatives is our next step in an attempt to discover a potential multi-target agent against coronavirus.

Quinazoline-Schiff base conjugates: in silico study and ADMET predictions as multi-target inhibitors of coronavirus (SARS-CoV-2) proteins
Mostafa A. Mansour, Asmaa M. AboulMagd and Hamdy M. Abdel-Rahman
RSC Adv., 2020,10, 34033-34045
DOI: 10.1039/D0RA06424F, Paper

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We are very pleased to introduce Dr Shuntaro Takahashi and Professor Naoki Sugimoto, first author and corresponding author of the paper ‘Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson–Crick rules‘. Their article has been very well received and handpicked by our reviewers and handling editors as one of our September HOT articles. The authors told us more about the work that went into this article and what they hope to achieve in the future. You can find out more about the authors and their article below and find more HOT articles in our online collection.

Meet the authors

Shuntaro Takahashi is an Associate Professor at the Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan. Dr. Takahashi earned his PhD degree at Tokyo Institute of Technology in 2007. After a period of research at Tokyo Institute of Technology as an Assistant Professor, he joined FIBER in 2012. He is currently studying the biophysics of nucleic acids in cells and the mechanism of molecular crowding for nucleic acid structures that affect cellular metabolism.

Professor Sugimoto received his PhD in 1985 from Kyoto University, Japan. After completing his postdoctoral work at the University of Rochester in the U.S.A., he became a faculty member at Konan University in Kobe, Japan in 1988. He has been a full professor since 1994 and a director at the Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University since 2003. He received The Imbach-Townsend Award from IS3NA in 2018. In 2020, he was awarded CSJ Awards from the Chemical Society of Japan. His research interests include biophysical chemistry, biomaterials, biofunctional chemistry, and biotechnology in the field of nucleic acid chemistry.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
We investigated the effect of chemical environments on gene replication of the virus RNA polymerase. This article provides insight into not only the evolution of life but also the mechanism of mutation of the virus genome including SARS-CoV-2.

How big an impact could your results potentially have?
Our results provide one story that the molecular environment could take part in the evolution of life by enhancing the replication error of genome sequences. Moreover, this study suggests the significance of molecular environments of patients’ cells for spreading viruses.

Could you explain the motivation behind this study?
The stability of the Watson-Crick base pair is NOT always the most stable, which can be perturbed by molecular environments. Therefore, we speculated that the replication of nucleic acids in the enzyme could also be affected by molecular environments and cause replication errors.

In your opinion, what are the key design considerations for your study?
The key design consideration of our study is to quantitatively understand the effect of molecular environments on the replication fidelity because the stability of nucleic acids structures depends on the physicochemical properties of the solution such as dielectric constant and water activity.

Which part of the work towards this paper proved to be most challenging?
For the reagents for the molecular environments, we used poly(ethylene glycol)s. Although these reagents were easy to tune the solution properties, the effect on RNA and protein were different and complex. The choice of suitable condition was very important for this kind of research.

What aspect of your work are you most excited about at the moment?
We were excited to find the replication rules became dependent on the stacking interactions more than Watson-Crick base pairing under molecular crowding conditions. This indicates that the replication error can be simply explained by the changes in dielectric constant.

What is the next step? What work is planned?
This study suggests that the rule of the base pairings can be differentiated under molecular crowding conditions. Thus, we will pursue the biological role of non-Watson-Crick base pairings such as Hoogsteen base pairs under different cellular conditions. We are also interested in the effect of molecular environments on the reaction of RNA-dependent RNA polymerase of Covid-19.

Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson–Crick rules
Shuntaro Takahashi, Hiromichi Okura, Pallavi Chilka, Saptarshi Ghosh and Naoki Sugimoto
RSC Adv., 2020,10, 33052-33058
DOI: 10.1039/D0RA06502A, Paper

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We are very pleased to introduce He Dong, the corresponding author of the paper ‘Modular design and self-assembly of multidomain peptides towards cytocompatible supramolecular cell penetrating nanofibers‘. Her article has been very well received and handpicked by our reviewers and handling editors as one of our September HOT articles.  He Dong was kind enough to tell us more about the work that went into this article and what she hopes to achieve in the future. You can find out more about the author and their article below and find more HOT articles in our online collection.

Meet the Author

He Dong obtained her PhD degree in organic chemistry at Rice University in 2008. After postdoc work at Emory University and the University of California at Berkeley, she started her independent career in the Department of Chemistry and Biomolecular Science at Clarkson University in 2012. She joined the Department of Chemistry and Biochemistry at the University of Texas at Arlington in 2018. Her research is focused on biomimetic design and supramolecular assembly of soft matter nanomaterials for anticancer and antimicrobial therapy development. She received a NSF Faculty Early Career Award for her work on the design and self-assembly of antimicrobial peptides. Recently, she was named as an Emerging Investigator of Journal of Materials Chemistry for the development of stimuli-responsive cell penetrating nanomaterials.

Dong Group

Graduate students Weike Chen (1st from the left), Ryan Madigan (2nd from the Left), Su Yang (2nd from the right) and Dr. He Dong (1st from the right) at the UTA Science & Engineering Innovation & Research Building.

Project defense of a high school student, Sidney Wang (2nd from the left) who was selected for research experiences of 2019 Welch Summer Scholar Program. Sidney’s project is to study the fundamental physicochemical property of supramolecular peptide nanofibers. Sidney’s mother (1st from the left), undergraduate student, Samuel Gardner (1st from the right) and Dr. Dong (2nd from the right) attended her defense.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
The efficacy of chemotherapy or gene therapy, in large part, depends on the ability of chemotherapeutics or genetic materials to cross the cell membrane to reach the cytoplasm. Designing nanomaterials that can facilitate intracellular delivery of therapeutics to the cytosol is of great interests from both fundamental research and practical point of view. This work is focused on a supramolecular approach for the design, and synthesis of supramolecular cell penetrating nanofibers (SCPNs) which have potent membrane activity and excellent cytocompatibility for intracellular delivery of therapeutics and/or imaging agents.

How big an impact could your results potentially have?
The success of the project will substantially advance our ability to develop peptide-based cell penetrating nanomaterials for a range of biomedical applications which required the delivery of therapeutics inside the cell. The range of molecular and supramolecular chemistry developed in this project will lead to a comprehensive fundamental understanding of the structure-activity relationship beyond the molecular level. The acquired knowledge will help build up a solid foundation for the rational design of supramolecular nanostructured materials, in particular nanofiber-based materials for other applications, not limited to drug/gene delivery in the biological arena. They can be potential used for vaccine delivery and antimicrobial materials design and development, all of which require potent cell penetrating activity.

Could you explain the motivation behind this study?
The discovery of cell penetrating peptides (CPPs) has great impacts on both fundamental and translational biomedical research due to their seemingly at will ability to transverse the cell membrane. However, most natural and synthetic CPPs suffer from poor stability against proteolysis and rapid in vivo clearance. Peptide self-assembly offers an effective method to generate supramolecular nanomaterials with improved stability, dynamic nanostructure and biological activity. In particular, the high aspect ratio peptide nanofibers showed good in vivo stability and have been extensively studied as functional scaffolds and for a variety of in vivo biomedical applications. Inspired by both natural CPPs and fibrous peptides, we build a novel class of supramolecular cell penetrating nanofibers (SCPNs) through the self-assembly of integrated cationic -sheet forming peptides to overcome the intrinsic limitation of traditional CPPs while having potent cell penetrating activity and minimum cytotoxicity.

In your opinion, what are the key design considerations for your study?
The key design considerations are on the modular design and self-assembly of MDPs to afford supramolecular assemblies with tunable nanostructure morphology and cationic domain conformational flexibility. The combined supramolecular structures and conformational flexibility of the cationic domain play dual roles in mediating the cell penetrating activity and therefore drug delivery efficacy.

Which part of the work towards this paper proved to be most challenging?
Understanding the correlation between structure and cell penetrating activity requires detailed structural characterization on both the molecular and supramolecular level. The biggest challenges that we overcome is the elucidation of the solution self-assembly states adopted by different supramolecular assemblies and further their structure-dependent membrane activity.

What aspect of your work are you most excited about at the moment?
From the fundamental self-assembly point of view, the work is novel and significant as it established a general peptide self-assembly mechanism by which SPCNs can be generated and optimized for both nanostructures and cell penetrating activity. From a broader viewpoint of biomedical application, these MDPs can be readily modified with various chemical functionalities, particular those served as stimuli-responsive chemical linkers that can respond to a range of disease-specific microenvironment to turn on/off the cell penetrating activity. Such efforts would be greatly beneficial for the development of smart SPCNs as disease-specific molecular therapy and imaging agents.

What is the next step? What work is planned?
The current work laid solid foundation for the synthesis of tumor microenvironment (such as pH, enzymes, ROS or hypoxia) responsive SCPNs which have tumor-specific cell penetrating activity. These “smart” tumor-responsive SCPNs would be great candidates to test the in vivo stability, targeting efficacy and overall therapeutic efficacy of SCPNs.

Modular design and self-assembly of multidomain peptides towards cytocompatible supramolecular cell penetrating nanofibers
Su Yang and He Dong
RSC Adv., 2020,10, 29469-29474
DOI: 10.1039/D0RA04748A, Paper

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We are very pleased to introduce Rajendra Joshi and the team of authors of the paper ‘Remdesivir-bound and ligand-free simulations reveal the probable mechanism of inhibiting the RNA dependent RNA polymerase of severe acute respiratory syndrome coronavirus 2‘. Their article has been very well received and handpicked by our reviewers and handling editors as one of our HOT articles. The team told us more about the work that went into this article and what they hope to achieve in the future. You can find out more about the authors and their article below and find more HOT articles in our online collection.

About Dr Rajendra Joshi

Dr. Rajendra Joshi received his Ph.D. in Biochemistry from National Chemical Laboratory, Pune, India in 1994. He has been associated with the area of Biotechnology & Bioinformatics for the about 28 years. He is presently serving as a Senior Director and Head of the Department, High Performance Computing-Medical and Bioinformatics Applications Group, at C-DAC, Pune.

His major area of expertise, is in the use of high performance parallel computers for biological research. His unique strength is in the form of good knowledge of biology and parallel computing. His main research interests include, molecular dynamics simulations of nucleic acids & proteins, genome sequence analysis, metabolic pathways and development of Problem Solving Environments. He has around 66 publications in internationally peer reviewed journals.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
Remdesivir, the emergency drug approved for treating COVID-19 patients helps in blocking the multiplication of SARS-CoV-2 virus. The action of this drug on the viral protein RNA dependent RNA polymerase was mimicked using computational methods, namely, molecular docking and molecular dynamics simulations.

How big an impact could your results potentially have?
The predicted mechanism of action of the drug, remdesivir, on the viral protein of SARS-CoV-2 would help in designing inhibitor molecules against the viruses. The drug target protein is the one, which is observed to be the most conserved among the coronavirus family. Statistically significant results produced through computational drug repurposing methods, add to the prediction accuracy of the drug-target interactions that are of major interest to develop therapeutics.

Could you explain the motivation behind this study?
The need to find the best solution against the global pandemic was the biggest motivation behind this study. This work was performed in the month of May 2020 and during that time, remdesivir, was being considered as one of the best solutions to treat the COVID-19 patients until the designing of the vaccine. Understanding the mechanism adopted by remdesivir would add to the information on the drug-action mechanism. This would be of importance to the experimental and pharmaceutical labs in the process of drug development.

In your opinion, what are the key design considerations for your study?
The key design considerations of our study was to mimic the RNA dependent RNA polymerase inhibition by remdesivir. Trying to understand the structure of RdRP and designing the best fit molecule which can inhibit the drug target with more potency. Being a part of, one of the High Performance Computing (HPC) groups in India, the entire computational study was designed around making the best use of the HPC technologies available to us.

Which part of the work towards this paper proved to be most challenging?
The research work involved many challenges since we had to design simulation systems with limited and evolving structural information of this virus. The major challenge being performing the computational drug repurposing studies in order to accelerate this research. In addition, the analytics involving statistical techniques for the identification of crucial residues and subdomains of the viral protein RNA dependent RNA polymerase also proved to be challenging.

What aspect of your work are you most excited about at the moment?
The mechanism of action and crucial interacting residues predicted through the computational methods in our present study were observed to match the experimental structures that are being elucidated for the RNA dependent RNA polymerase of the SARS-CoV-2.

What is the next step? What work is planned?
The work in this article dealt with remdesivir action in inhibiting the RNA dependent RNA polymerase of SARS-CoV-2. Besides remdesivir, other nucleotide analogues are also known to inhibit RdRP from the other coronaviruses. Hence, we have planned to study the inhibitory mechanism of other nucleotide/nucleoside analogues namely, favipiravir, galidesivir, lamivudine, ribavirin and sofosbuvir in their active metabolite form. This work is currently being targeted using molecular docking and molecular dynamics simulations. We have planned to understand the conformational changes that the RdRP undergoes on binding to natural nucleotides and their analogues. This information may help in designing of better nucleotide analogues.

One more aspect we plan to study is the role of phytochemicals from medicinal plants that are known to be used as a treatment for respiratory ailments. All the data obtained through simulations has been thoroughly sampled and analyzed using statistically significant methods, such as, principal component analysis and Markov state modeling analysis.

Remdesivir-bound and ligand-free simulations reveal the probable mechanism of inhibiting the RNA dependent RNA polymerase of severe acute respiratory syndrome coronavirus 2
Shruti Koulgi, Vinod Jani, Mallikarjunachari V. N. Uppuladinne, Uddhavesh Sonavane and Rajendra Joshi
RSC Adv., 2020,10, 26792-26803
DOI: 10.1039/D0RA04743K, Paper

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We are very pleased to introduce Marisa G. Santibáñez-Morán (first author), José Medina-Franco (corresponding author) and the team behind the paper ‘Consensus virtual screening of dark chemical matter and food chemicals uncover potential inhibitors of SARS-CoV-2 main protease‘. Their article has been very well received and handpicked by our reviewers and handling editors as one of our HOT articles. The team told us more about the work that went into this article and what they hope to achieve in the future. You can find out more about the authors and their research at DIFACQUIM, Computer-aided drug-design at UNAM, and find more HOT articles in our online collection.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
Our article looks for molecules in food chemicals or dark chemical matter (molecules that had not shown activity in 100 or more high-throughput screening assays) that are prospective inhibitors of the SARS-CoV-2 Main protease.

How big an impact could your results potentially have?
It could point to SARS-CoV-2 inhibitors that might otherwise have been overlooked. We would be glad if other research groups will be interested in the computational hits we made publicly available and further analyzed them in experimental assays.

Could you explain the motivation behind this study?
COVID-19 is currently affecting all aspects of human life. Our research group works on computer-aided drug design, and we had previously worked on drug repurposing. We felt that we could and should contribute to the collaborative efforts of scientists from all around the world.

In your opinion, what are the key design considerations for your study?
One was the selection of the molecular libraries where we looked for potential inhibitors. These comprise compounds that recent studies on SARS-CoV-2 have analyzed on a limited basis. Additionally, a large number of these molecules are ready to be tested in experimental assays. Moreover, there are currently numerous papers that reported favorable molecular docking results. However, selecting compounds that would have satisfactory potency and biopharmaceutical results in experimental settings is not trivial. Therefore, we ranked the compounds considering positive results by two molecular docking programs, Machine learning predictions, commercial availability, and ADMETox properties.

Which part of the work towards this paper proved to be most challenging?
First, to select a target and molecular queries for the structural similarity analyses. The latter should include structurally diverse and promising compounds. Another challenge was to create a classification method that helps us select compounds with better possibilities for drug development.

What aspect of your work are you most excited about at the moment?
I am excited about the possibility of finding supporting information about the activity of food chemicals against SARS-CoV-2. I believe that this could result in the development of nutraceuticals with inhibitory activity against the SARS-CoV-2 virus.

What is the next step? What work is planned?
We are waiting for the experimental results of 3 compounds that are being tested by our collaborators in North Carolina. We are also working on another manuscript that explores a broader region of the chemical space. And we hope that we could form new collaborations with RSC Advances readers.

Consensus virtual screening of dark chemical matter and food chemicals uncover potential inhibitors of SARS-CoV-2 main protease
Marisa G. Santibáñez-Morán, Edgar López-López, Fernando D. Prieto-Martínez, Norberto Sánchez-Cruz and José L. Medina-Franco
RSC Adv., 2020,10, 25089-25099
DOI: 10.1039/D0RA04922K, Paper

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We are very pleased to introduce Pavel Bobal, Jan Otevrel and David Svestka, the authors of the paper ‘One-pot method for the synthesis of 1-aryl-2-aminoalkanol derivatives from the corresponding amides or nitriles‘. Their article has been very well received and handpicked by our reviewers and handling editors as one of our HOT articles.  The team told us more about the work that went into this article and what they hope to achieve in the future. You can find out more about the authors and their article below and find more HOT articles in our online collection.

Meet the Authors

	Pavel Bobal studied organic chemistry at Slovak Technical University, Bratislava, Slovakia, where he received his doctoral degree in 1996. He spent 3 years between 1995 and 1998 as a postdoc at the University of Neuchatel, Switzerland (Prof. Neier) and additional 3 years at the University of Nevada, Reno, USA (Prof. Lightner). From 2001 to 2009 he worked in the pharmaceutical industry (R&D). In 2009 he became an assistant professor and then in 2019 an associate professor at Faculty of Pharmacy, UVPS Brno, Czech Republic. Since 2020 this faculty has been reestablished as a part of Masaryk University, Brno, Czech Republic.
	Jan Otevrel was a former Ph.D. student of Pavel Bobal, he received his doctoral degree in 2017 and then became an assistant professor at the same university. During his Ph.D. he spent 3 months at Justus Liebig University, Giessen, Germany (Prof. Hrdina) and he will soon (this year) start a postdoc position at Johannes Kepler University, Linz, Austria (Prof. Waser). He has discovered and co-developed the process published in the current study.
	David Svestka received his master’s degree in 2019 at UVPS Brno, Czech Republic. He is currently a Ph.D. student in the Pavel Bobal’s laboratory and participated in the development of the present method.

Could you briefly explain the focus of your article to the non-specialist (in one or two sentences only) and why it is of current interest?
Our paper describes a new method for synthesis of vicinal amino alcohols from the respective amides or nitriles by a simple set of reaction conditions. Amino alcohols are compounds of high interest in many branches of chemistry.

How big an impact could your results potentially have?
It is always hard to predict feedback of the scientific article. However, from our perspective, we would be glad if the developed process will find place in syntheses of vicinal amino alcohols conducted at research laboratories and if the readers of RSC Advances will appreciate efforts which we have invested in this paper.

Could you explain the motivation behind this study?
Due to our continuous interest in the organocatalyzed aldol-type reactions, we have been exploring syntheses of numerous chiral auxiliaries for the catalyst design and screening. These long-term endeavor paved a way for our current unexpected discovery.

In your opinion, what are the key design considerations for your study?
The key consideration in this study is to use an old and well-known reagent in a new context to reveal the novel and yet unexplored reactivity.

Which part of the work towards this paper proved to be most challenging?
The methodological articles in organic synthesis usually share the common structure such as the optimization section, determination of the substrate scope, and a relevant synthetic application of the method. Thus from the initial interesting observation, it is often quite a long journey towards the good scientific paper. Honestly, one of the most challenging parts of the above article was to establish a plausible mechanism of the reaction and to support it with enough evidence.

What aspect of your work are you most excited about at the moment?
One of the most exciting moments of this discovery was to figure out that benzylic oxidation can occur even under reduction conditions, which is somewhat counter-intuitive. Indeed, sodium bis(methoxyethoxy)aluminum hydride gave us a great lecture that more than 50 years old and almost comprehensively explored reagent is still able to surprise.

What is the next step? What work is planned?
We will continue with our work in organic synthesis and medicinal chemistry and we will look forward to the new and especially the unexpected chemical discoveries.

One-pot method for the synthesis of 1-aryl-2-aminoalkanol derivatives from the corresponding amides or nitriles
Jan Otevrel, David Svestka and Pavel Bobal
RSC Adv., 2020,10, 25029-25045
DOI: 10.1039/D0RA04359A, Paper

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