Targeting Kaposi's sarcoma associated herpesvirus encoded protease (ORF17) by a lysophosphatidic acid molecule for treating KSHV associated diseases.

Kaposi's sarcoma associated herpesvirus (KSHV) is causative agent of Kaposi's sarcoma, Multicentric Castleman Disease and Pleural effusion lymphoma. KSHV-encoded ORF17 encodes a protease which cleaves -Ala-Ala-, -Ala-Ser- or -Ala-Thr-bonds. The protease plays an important role in assembly and maturation of new infective virions. In the present study, we investigated expression pattern of KSHV-encoded protease during physiologically allowed as well as chemically induced reactivation condition. The results showed a direct and proportionate relationship between ORF17 expression with reactivation time. We employed virtual screening on a large database of natural products to identify an inhibitor of ORF17 for its plausible targeting and restricting Kaposi's sarcoma associated herpesvirus assembly/maturation. A library of 307,814 compounds of biological origin (A total 481,799 structures) has been used as a screen library. 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-(1'-myo-inositol) was highly effective against ORF17 in in-vitro experiments. The screened compound was tested for the cytotoxic effect and potential for inhibiting Kaposi's sarcoma associated herpesvirus production upon induced reactivation by hypoxia, TPA and butyric acid. Treatment of reactivated KSHV-positive cells with 1-oleoyl-2-hydroxy-sn-glycero-3-phospho-(1'-myo-inositol) resulted in significant reduction in the production of Kaposi's sarcoma associated herpesvirus. The study identified a lysophosphatidic acid molecule for alternate strategy to inhibit KSHV-encoded protease and target Kaposi's sarcoma associated herpesvirus associated malignancies.

PheroxyPyrabenz and Carbopyrropyridin against major proteins of SARS CoV-2: a comprehensive in-silico molecular docking and dynamics simulation studies.

The pandemic that started in 2020 left us with so much information about viruses and respiratory diseases, and the cause behind it was severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The world is still recovering, which costs so many economic and other indirect disasters; despite that, no medications are available on the market. Although the WHO approved a few vaccines on an emergency basis, the remarks and the reinfection chances are still under investigation, and a few pharmaceutical companies are also claiming that a few medications can be effective. However, there is no situation in control. SARS CoV-2 mutates and comes in different forms, making the situation unpredictable. In this study, we have screened the complete Asinex's BioDesign library, which contains 170,269 compounds, and shorted the data against the docking score that helps in the identification of 4-[5-(3-Ethoxy-4-hydroxyphenyl)-1-(2-hydroxyethyl)-1H-pyrazol-3-yl]-1, 2-benzenediol (PheroxyPyrabenz) and 1-[(3R,4R)-1-(5-Aminopentanoyl)-4-hydroxy-3-pyrrolidinyl]-1H-pyrrolo[2,3-b]pyridine-4-carboxamide (Carbopyrropyridin) as a significant drug candidate that can work against the multiple proteins of the SARS CoV-2 resulting in seizing the complete biological process of the virus. Further, the study extended to Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and molecular dynamics (MD) simulation of both the compounds with their complexity. The complete workflow of the study has shown satisfactory results, and both drug candidates can potentially stop the hunt for drugs against this virus after its experimental validation. Further, we checked both compounds' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, showing case-proof validatory results.Communicated by Ramaswamy H. Sarma.

Developing and Testing Methylated Nano-Structured Dipeptides that Inhibit Src Kinase Activity In Vitro for Anti-Cancer Applications.

Here, with the aim of developing a novel anti-cancer treatment, seven dipeptides were designed that contained methylated tryptophan and/or methylated arginine and were produced using Fmoc solid-phase peptide synthesis. Overexpression of the Src tyrosine kinase enzyme has been implicated in the development of different cancers. Dipeptides containing unnatural amino acids such as methylated arginine (RCH3), dimethylated arginine (R(CH3)2), and/or methylated tryptophan (WCH3) residues have earlier been shown to inhibit Src kinase. In this study, three such dipeptides, W-RCH3, WCH3-RCH3, and W-R(CH3)2, were tested using acellular assays and were found to have IC50 values (the concentration at which 50% inhibition occurs) of 510 nM, 916 nM, and 1 µM, respectively. These values were comparable to those obtained for cyclic penta- to nano-W-R peptides ([W-R]5-[W-R]9) synthesized in previous studies. However, the unmethylated versions of the dipeptides did not show any inhibitory activity against Src kinase. All of these dipeptides (50 µM) did not show any cytotoxicity after incubation up to 72 h with three different cancer cell lines, including leukemia (CCRF-CEM), breast adenocarcinoma (MDA-MB-231), and ovarian adenocarcinoma (SK-OV-3) cell lines, indicating the limited permeability of the peptides through the cell membrane. Therefore, further study is needed to improve the permeability of these peptides for anticancer applications, such as by using a peptide carrier or additional peptide functionalization. In summary, this study provides a protocol to synthesize and test peptides that inhibit Src kinase activity, and thus possess promising anticancer ability, as demonstrated using acellular and cellular assays.

Identification of compelling inhibitors of human norovirus 3CL protease to combat gastroenteritis: A structure-based virtual screening and molecular dynamics study.

Human noroviruses (NV) are the most prevalent cause of sporadic and pandemic acute gastroenteritis. NV infections cause substantial morbidity and death globally, especially amongst the aged, immunocompromised individuals, and children. There are presently no authorized NV vaccines, small-molecule therapies, or prophylactics for humans. NV 3 C L protease (3CLP) has been identified as a promising therapeutic target for anti-NV drug development. Herein, we employed a structure-based virtual screening method to screen a library of 700 antiviral compounds against the active site residues of 3CLP. We report three compounds, Sorafenib, YM201636, and LDC4297, that were revealed to have a higher binding energy (BE) value with 3CLP than the control (Dipeptidyl inhibitor 7) following a sequential screening, in-depth molecular docking and visualization, physicochemical and pharmacological property analysis, and molecular dynamics (MD) study. Sorafenib, YM201636, and LDC4297 had BEs of -11.67, -10.34, and -9.78 kcal/mol with 3CLP, respectively, while control had a BE of -6.38 kcal/mol. Furthermore, MD simulations of the two best compounds and control were used to further optimize the interactions, and a 100 ns MD simulation revealed that they form stable complexes with 3CLP. The estimated physicochemical, drug-like, and ADMET properties of these hits suggest that they might be employed as 3CLP inhibitors in the management of gastroenteritis. However, wet lab tests are a prerequisite to optimize them as NV 3CLP inhibitors.

Inhibiting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants: Targeting the Spike and Envelope Proteins Using Nanomaterial Like Peptides.

Coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused significant death, economic crisis, and the world to almost completely shut down. This present study focused on targeting the novel SARS-CoV-2 envelope protein, which has not been frequently mutating, and the S protein with a much larger peptide capable of inhibiting virus-mammalian cell attraction. In doing so, molecular dynamics software was used here to model six peptides including: NapFFTLUFLTUTE, NapFFSLAFLTATE, NapFFSLUFLSUTE, NapFFTLAFLTATE, NapFFSLUFLSUSE, and NapFFMLUFLMUME. Results showed that two of these completely hydrophobic peptides (NapFFTLUFLTUTE and NapFFMLUFLMUME) had a strong ability to bind to the virus, preventing its binding to a mammalian cell membrane, entering the cell, and replicating by covering many cell attachment sites on SARS-CoV-2. Further cell modeling results demonstrated the low toxicity and suitable pharmacokinetic properties of both peptides making them ideal for additional in vitro and in vivo investigation. In this manner, these two peptides should be further explored for a wide range of present and future COVID-19 therapeutic and prophylactic applications.

Targeting the Conserved Sequence of the Substrate for the Proteinase of Severe-Acute-Respiratory-Syndrome-Coronavirus-2 (SARS-CoV-2) Using Nano-Networks: Efficacy, Stability, and No Cytotoxicity.

Herein, we designed a nano peptide that contains three important motifs for targeting the chemotrypsin-like cysteine protease (3CLpro) which is the enzyme responsible for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) replication. The novel nano peptide contains the Nap Phe-Phe motif that is responsible for peptide self-assembly, an octapeptide (Ser-Ala-Val-Leu-Gln-Ser-Gly-Phe) motif where the enzyme recognizes the substrate and induces enzyme sensitivity, and a tetrapeptide motif which is positively charged containing the peptide (Lys)4 that facilitates penetration into a cell. The nano peptide was characterized using Proton Nuclear Magnetic Resonance (H-NMR) and Liquid Chromatography-Mass Spectrometry (LC-MS) to confirm its structure. In vitro results showed that the presently formulated nano peptide was not cytotoxic to fibroblasts for up to 72 hours, bound to 3CLpro, inhibited SARS-CoV-2 Omicron variant virus replication, and was stable for binding for up to one week in culture. In this manner, this timely study demonstrates that this novel nano peptide should be studied for a wide range of Coronavirus Disease (COVID-19) prophylactic or therapeutic applications.

The promising use of nano-molecular imprinted templates for improved SARS-CoV-2 detection, drug delivery and research.

Molecular imprinting (MI) is a technique that creates a template of a molecule for improving complementary binding sites in terms of size and shape to a peptide, protein, bacteria, mammalian cell, or virus on soft materials (such as polymers, hydrogels, or self-assembled materials). MI has been widely investigated for over 90 years in various industries but is now focused on improved tissue engineering, regenerative medicine, drug delivery, sensors, diagnostics, therapeutics and other medical applications. Molecular targets that have been studied so far in MI include those for the major antigenic determinants of microorganisms (like bacteria or viruses) leading to innovations in disease diagnosis via solid-phase extraction separation and biomimetic sensors. As such, although not widely investigated yet, MI demonstrates much promise for improving the detection of and treatment for the current Coronavirus Disease of 2019 (COVID-2019) pandemic as well as future pandemics. In this manner, this review will introduce the numerous applications of MI polymers, particularly using proteins and peptides, and how these MI polymers can be used as improved diagnostic and therapeutic tools for COVID-19.

The Physical Properties of Tripeptide Stereocomplex Nano-Formations.

The fast-growing use of supramolecular hydrogelators as biomaterials for a variety of applications, ranging from wound healing to drug delivery to tissue engineering, has highlighted the importance of synthetic design over recent years. Here, we report a new class of nanosheet stereocomplexes in aqueous solution and at physiological conditions (i. e., pH7.4), which are formed by physically mixing right- and left-handed tripeptide supramolecular hydrogelators without any external stimulus. Such tripeptides were obtained by incorporating either α-aminoisobutyric acid (Aib, U) or alanine (Ala, A) at the C-terminus or middle position of known peptide hydrogelators containing naphthalene and two phenylalanine residues. For hydrogels of these peptides, our results show that their morphologies and physical properties changed upon mixing with the L- and D-forms of the peptides forming suspension stereocomplexes. These interactions reduced molecular mobility by forming new structures with new properties and, therefore, increased the thermal stability of the compound promising for numerous medical applications.

Introducing Unnatural Amino Acids-Containing Tripeptides as Antimicrobial and Anticancer Agents.

Hydrogelators are crosslinked polymeric networks that are capable of holding large amounts of water by surface tension. High-water absorption capacity makes hydrogels readily biocompatible and, thus, more attractive for medical applications. The objective of the present in vitro study was to test supramolecular hydrogelators for multiple biomedical applications: bacterial- and cancer-related diseases. Four naphthalene-tripeptides and their D-enantiomers were synthesized using an Fmoc Solid Phase Peptide Synthesis strategy and were tested for their activity on normal and cancer cells as well as bacteria. Here, the D-enantiomer of alanine containing tripeptides at a concentration of 0.25 wt% inhibited the growth of Staphylococcus epidermidis. Moreover, cytotoxicity assays showed that naphthalene containing tripeptides possessing α-aminoisobutyric acid (Aib, U) between the two phenylalanine groups (i.e., NapFUF) selectively decreased against melanoma cancer cell viability at 0.25 wt% compared to controls (no additives) over a 24 h time period. These results suggest, for the first time, that naphthalene-tripeptides containing α-aminoisobutyric acid or alanine have numerous potential uses for diverse medical applications, in particular for fighting cancer and bacterial infections.