Processes

Research

11 pages, 2372 KiB

Open AccessArticle

Dataset of 3β-Corner and 3β-Corner-like Structures

by Vladimir R. Rudnev, Liudmila I. Kulikova, Kirill S. Nikolsky, Denis V. Petrovsky, Alexander A. Stepanov, Kristina A. Malsagova and Anna L. Kaysheva

Processes 2023, 11(2), 368; https://doi.org/10.3390/pr11020368 - 24 Jan 2023

Viewed by 939

Abstract

The study is devoted to the creation of a dataset of protein structural motifs of the 3β-corner type. The relevance and importance of creating a dataset of 3β-corners is determined by the fact that this structure can be an embryo or a ready-made [...] Read more.

The study is devoted to the creation of a dataset of protein structural motifs of the 3β-corner type. The relevance and importance of creating a dataset of 3β-corners is determined by the fact that this structure can be an embryo or a ready-made structural block in the process of protein folding, and can also act as an independent object of research in the field of structural biology. The dataset also contains 3β-corner-like structures that are geometrically similar to 3β-corners. The dataset consists of 45,896 structures. For each motif, its characteristics are presented: the name of the protein in which the 3β-corner is recognized, the method and resolution of the protein structure, the coordinates of localization in the protein, the secondary structure of the amino acid sequence, the gyration radius, the solvent-accessible area, and the composition of the elements of the secondary structure. The dataset will allow a comprehensive study of structures on a large scale and advance the understanding of the features and patterns of their structural organization. Full article

(This article belongs to the Special Issue Protein Biosynthesis and Drug Design & Delivery Processes)

► Show Figures

Figure 1

18 pages, 4319 KiB

Open AccessArticle

Anandamide Reuptake Inhibitor (VDM11) as a Possible Candidate for COVID-19 Associated Depression; a Combination of Network Pharmacology, Molecular Docking and In Vivo Experimental Analysis

by Sami I. Alzarea, Sumera Qasim, Muhammad Afzal, Omar Awad Alsaidan, Hassan H. Alhassan, Metab Alharbi, Mohammed Alqinyah and Fahaad S. Alenazi

Processes 2023, 11(1), 143; https://doi.org/10.3390/pr11010143 - 03 Jan 2023

Cited by 3 | Viewed by 1801

Abstract

Objective: Post-COVID 19 depression has gained much attention due to the increasing percentage of depressive symptoms reported by COVID-19 survivors. Among many factors postulated to be responsible for this depression, neuroinflammation gained the most attention. Therefore, in current work, we selected an anandamide [...] Read more.

Objective: Post-COVID 19 depression has gained much attention due to the increasing percentage of depressive symptoms reported by COVID-19 survivors. Among many factors postulated to be responsible for this depression, neuroinflammation gained the most attention. Therefore, in current work, we selected an anandamide reuptake inhibitor, VDM11, as a possible candidate for managing post-COVID depression. Methods: The role of VDM11 in attenuating neuroinflammation was established by using network pharmacology, molecular docking, and an in vivo LPS-induced depression model. Results: The results of network pharmacology revealed that among all the genes that can be targeted by VDM11, 47 genes were directly linked to the pathophysiology of depression. Additionally, on the basis of protein–protein interaction (PPI) analysis, the top 10 hub genes probably responsible for VDM11 antidepressant attribute were screened. These genes include MAPK3, TNF-α, IL-1β, IL-6, PPARG, MAPK1, CNR1, MTOR, NR3C1, and IGF1R. These genes were also enriched in GO and KEGG analysis. Molecular docking was carried out with top five hub genes screened by PPI network and KEGG analysis which showed that VDM11 interacts well with these targets. The antidepressant potential of VDM11 was also assessed by employing a LPS-induced depression model. Animals provided with VDM11 demonstrated increased exploration time and spontaneous alterations in elevated plus and Y maze models. Additionally, the level of astrocyte marker GFAP, microglia marker CD11b, and proinflammatory cytokines, including TNFα, IL-1β, and IL-6, in the hippocampus were significantly reduced by VDM11, further strengthening its role in neuroinflammation. Conclusion: VDM11, an anandamide reuptake inhibitor, might serve as a possible candidate for post-COVID depression, probably by modulating neuroinflammation. However, detailed pharmacological studies are required to validate these outcomes. Full article

(This article belongs to the Special Issue Protein Biosynthesis and Drug Design & Delivery Processes)

► Show Figures

Graphical abstract

13 pages, 1779 KiB

Open AccessArticle

Biological Role of the 3β-Corner Structural Motif in Proteins

by Vladimir R. Rudnev, Denis V. Petrovsky, Kirill S. Nikolsky, Liudmila I. Kulikova, Alexander A. Stepanov, Kristina A. Malsagova, Anna L. Kaysheva and Alexander V. Efimov

Processes 2022, 10(11), 2159; https://doi.org/10.3390/pr10112159 - 22 Oct 2022

Cited by 2 | Viewed by 1493

Abstract

In this study, we analyze the occurrence of the unique structural motif, the 3β-corner, belonging to the Structural Classification of Proteins (SCOP) folds, in proteins of various origins. We further assess the structural and functional role of this motif as well as the [...] Read more.

In this study, we analyze the occurrence of the unique structural motif, the 3β-corner, belonging to the Structural Classification of Proteins (SCOP) folds, in proteins of various origins. We further assess the structural and functional role of this motif as well as the clustering of the biological functions of proteins in which it occurs. It has been shown previously that the 3β-corner occurs with different probabilities in all beta proteins, alpha and beta proteins (α + β and α/β), and alpha classes occur most often in the composition of β-proteins. The 3β-corner is often found as a building block in protein structures, such as β-barrels, -sandwiches, and -sheets/-layers. Full article

(This article belongs to the Special Issue Protein Biosynthesis and Drug Design & Delivery Processes)

► Show Figures

Figure 1

9 pages, 991 KiB

Open AccessArticle

Evaluation of Oleic Acid and Polyethylene Glycol Monomethyl Ether Conjugate (PEGylated Oleic Acid) as a Solubility Enhancer of Furosemide

by Rahul S. Kalhapure, Pradeep Kumar Bolla, Sai HS. Boddu and Jwala Renukuntla

Processes 2019, 7(8), 520; https://doi.org/10.3390/pr7080520 - 07 Aug 2019

Cited by 2 | Viewed by 4061

Abstract

Poor aqueous solubility limits the therapeutic efficacy of many marketed and investigational drugs. Synthesis of new drugs with improved solubility is challenging due to time constraint and expenses involved. Therefore, finding the solubility enhancers for existing drugs is an attractive and profitable strategy. [...] Read more.

Poor aqueous solubility limits the therapeutic efficacy of many marketed and investigational drugs. Synthesis of new drugs with improved solubility is challenging due to time constraint and expenses involved. Therefore, finding the solubility enhancers for existing drugs is an attractive and profitable strategy. In this study, PEGylated oleic acid (OA-mPEG₅₀₀₀), a conjugate of oleic acid and mPEG₅₀₀₀ was synthesized and evaluated as a solubilizer for furosemide. OA-mPEG₅₀₀₀ was evaluated as a nanocarrier for furosemide by formulating polymersomes. Solubility of furosemide in milli-Q water and aqueous OA-mPEG₅₀₀₀ solution was determined using shake flask method. At 37 °C, the solubility of furosemide in OA-mPEG5000 (1% w/w) and milli-Q water was 3404.7 ± 254.6 µg/mL and 1020.2 ± 40.9 µg/mL, respectively. Results showed there was a 3.34-fold increase in solubility of furosemide in OA-mPEG₅₀₀₀ compared to water at 37 °C. At 25 °C, there was a 3.31-fold increase in solubilization of furosemide in OA-mPEG₅₀₀₀ (1% w/w) (90.0 ± 1.45 µg/mL) compared to milli-Q water (27.2 ± 1.43 µg/mL). Size, polydispersity index and zeta potential of polymersomes ranged from 85–145.5 nm, 0.187–0.511 and −4.0–12.77 mV, respectively. In-vitro release study revealed a burst release (71%) within 1 h. Significant enhancement in solubility and formation of polymersomes suggested that OA-mPEG₅₀₀₀ could be a good solubilizer and nanocarrier for furosemide. Full article

(This article belongs to the Special Issue Protein Biosynthesis and Drug Design & Delivery Processes)

► Show Figures

Figure 1

12 pages, 3073 KiB

Open AccessArticle

Preparation and Characterization of Furosemide-Silver Complex Loaded Chitosan Nanoparticles

by Victor A. Rodriguez, Pradeep Kumar Bolla, Rahul S. Kalhapure, Sai Hanuman Sagar Boddu, Rabin Neupane, Julian Franco and Jwala Renukuntla

Processes 2019, 7(4), 206; https://doi.org/10.3390/pr7040206 - 11 Apr 2019

Cited by 10 | Viewed by 3335

Abstract

Antibiotic-resistant bacteria may result in serious infections which are difficult to treat. In addition, the poor antibiotic pipeline has contributed to the crisis. Recently, a complex of furosemide and silver (Ag-FSE) has been reported as a potential antibacterial agent. However, its poor aqueous [...] Read more.

Antibiotic-resistant bacteria may result in serious infections which are difficult to treat. In addition, the poor antibiotic pipeline has contributed to the crisis. Recently, a complex of furosemide and silver (Ag-FSE) has been reported as a potential antibacterial agent. However, its poor aqueous solubility is limiting its activity. The purpose of this study was to encapsulate Ag-FSE into chitosan nanoparticles (CSNPs) and evaluate antibacterial efficacy. Ag-FSE CSNPs were prepared using an ionic gelation technique. The particle size, polydispersity index, and zeta potential of Ag-FSE CSNPs were 197.1 ± 3.88 nm 0.234 ± 0.018 and 36.7 ± 1.78 mV, respectively. Encapsulation efficiency was 66.72 ± 4.14%. In vitro antibacterial activity results showed that there was 3- and 6-fold enhanced activity with Ag-FSE CSNPs against E. coli and S. aureus, respectively. Results also confirmed that Ag-FSE CSNPs showed ~44% release within 4 h at pH 5.5 and 6.5. Moreover, release from the CSNPs was sustained with a cumulative release of ~75% over a period of 24 h. In conclusion, encapsulation of Ag-FSE into CSNPs resulted in significant improvement of antibacterial efficacy with a sustained and pH-sensitive release. Therefore, Ag-FSE CSNPs can be considered as a potential novel antibacterial agent against bacterial infections. Full article

(This article belongs to the Special Issue Protein Biosynthesis and Drug Design & Delivery Processes)

► Show Figures

Graphical abstract

Review

Jump to: Research, Other

13 pages, 1492 KiB

Open AccessReview

The Importance of Drug Delivery in the Clinical Development and Lifecycle of Drug Products with Examples from Authorised Medicinal Products

by Maria Malamatari

Processes 2023, 11(10), 2919; https://doi.org/10.3390/pr11102919 - 05 Oct 2023

Viewed by 1512

Abstract

Drug delivery systems (DDS) are formulations or devices that enable the introduction of a therapeutic into the body and its delivery to its target site, potentially enhancing its efficacy and safety. Advances in formulation approaches related to the enhancement of solubility, permeability and [...] Read more.

Drug delivery systems (DDS) are formulations or devices that enable the introduction of a therapeutic into the body and its delivery to its target site, potentially enhancing its efficacy and safety. Advances in formulation approaches related to the enhancement of solubility, permeability and thus bioavailability of drugs have already been successfully implemented by the pharmaceutical industry. This review highlights the importance of formulations/DDS in the clinical development and the lifecycle of drug products. Examples from already authorised drug products have been used to showcase how the development of appropriate formulations/DDS could deliver drugs to the site of action (e.g., pulmonary and nasal drug delivery) and enhance patient adherence to medication (e.g., long-acting injectables, 3D-printed tablets). Moreover, examples from authorised products have been provided to highlight how formulation can improve safety (e.g., liposomes, abuse-deterrent opioid formulations) and efficacy (e.g., albumin-based nanoparticles, permeation enhancers for oral delivery of peptides). Full article

(This article belongs to the Special Issue Protein Biosynthesis and Drug Design & Delivery Processes)

► Show Figures

Figure 1

Other

Jump to: Research, Review

5 pages, 909 KiB

Open AccessFeature PaperCommentary

Untangling the Potential of Carbon Quantum Dots in Neurodegenerative Disease

by Lindsey Jung, Prakash Narayan, Sreeprasad T. Sreenivasan and Mahesh Narayan

Processes 2020, 8(5), 599; https://doi.org/10.3390/pr8050599 - 18 May 2020

Cited by 7 | Viewed by 4605

Abstract

The transitioning of carbon quantum dot (cQD) applications from electrochemistry, catalysis and environmental sensing to biomedicine represents an important milestone in its 15-year history; a bellwether for its yet-unrealized potential in interventional biology, imaging, diagnostics, prophylaxis and therapy. However, despite the significant advances [...] Read more.

The transitioning of carbon quantum dot (cQD) applications from electrochemistry, catalysis and environmental sensing to biomedicine represents an important milestone in its 15-year history; a bellwether for its yet-unrealized potential in interventional biology, imaging, diagnostics, prophylaxis and therapy. However, despite the significant advances made over the last decade in several areas of the cQD domain, our knowledge of the exact chemical ipseity of cQDs at the Angstrom level remains either in its infancy or is largely ignored. The imminent crossing over of cQDs into biological systems and into the blood–brain barrier demands attention to the critical, yet unmet, need to resolve the inherent heterogeneity in cQD preparations and their separation into purified conformers, to identify the issues associated with potential cytotoxicity as well as to examine their bioavailability. Perhaps most importantly, and ironically neglected as well, is the compelling urgency to obtain an atomic- and molecular-level understanding of cQD’s interactions with biological receptors; a demand that requires absolute knowledge of its structure, chemistry and aspects therein. The need for the total chemical mapping of cQDs, with Angstrom-level resolution, remains the unrealized cornerstone to tailoring its specificity for its designated use in preclinical and clinical trials. Full article

(This article belongs to the Special Issue Protein Biosynthesis and Drug Design & Delivery Processes)

► Show Figures

Figure 1

6 pages, 1305 KiB

Open AccessFeature PaperOpinion

Influence of Carbon Quantum Dots on the Biome

by Jose Peralta-Videa, Sreeprasad T Sreenivasan and Mahesh Narayan

Processes 2020, 8(4), 445; https://doi.org/10.3390/pr8040445 - 10 Apr 2020

Cited by 9 | Viewed by 4202

Abstract

The latest class of engineered nanomaterials, viz., carbon quantum dots (CQDs), has attracted attention because they are synthesized through green chemical procedures and from organic waste matter. The synthesis of these nano-sized particles synthesized from biomass such as fruit peel and other organic [...] Read more.

The latest class of engineered nanomaterials, viz., carbon quantum dots (CQDs), has attracted attention because they are synthesized through green chemical procedures and from organic waste matter. The synthesis of these nano-sized particles synthesized from biomass such as fruit peel and other organic matter results in mixtures of CQD species that differ in chemical identity, activity and photo-physical properties. Generally used collectively as chemically heterogeneous ensemble, they have already had an impact on multiple sectors of our environment by use as wastewater sensors, switches, model agro-fertilizers, and in biomedicine. The transitioning of their applications to crops is an important crossover point that calls for an accurate and detailed assessment of their genomic, proteomic, and metabolomics impact on agriculturally important crops and produce. We review the current status of CQDs vis-à-vis their impact on the biosphere via recent model studies and comment on the knowledge gaps that need to be bridged to ensure their safe use in agronomy. A detailed knowledge of their impact on aquatic systems and the food-chain is critical for human and environmental safety and sustainability. Full article

(This article belongs to the Special Issue Protein Biosynthesis and Drug Design & Delivery Processes)

► Show Figures

Scheme 1

Journal Menu

Journal Browser

Protein Biosynthesis and Drug Design & Delivery Processes

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Published Papers (8 papers)

Research

Review

Other

Further Information

Guidelines

MDPI Initiatives

Follow MDPI