Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids.

CRISPR-Cas-based diagnostics have the potential to elevate nucleic acid detection. CRISPR-Cas systems can be combined with a pre-amplification step in a one-pot reaction to simplify the workflow and reduce carryover contamination. Here, we report an engineered Cas12b with improved thermostability that falls within the optimal temperature range (60°C-65°C) of reverse transcription-loop-mediated isothermal amplification (RT-LAMP). Using de novo structural analyses, we introduce mutations to wild-type BrCas12b to tighten its hydrophobic cores, thereby enhancing thermostability. The one-pot detection assay utilizing the engineered BrCas12b, called SPLENDID (single-pot LAMP-mediated engineered BrCas12b for nucleic acid detection of infectious diseases), exhibits robust trans-cleavage activity up to 67°C in a one-pot setting. We validate SPLENDID clinically in 80 serum samples for hepatitis C virus (HCV) and 66 saliva samples for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high specificity and accuracy. We obtain results in as little as 20 min, and with the extraction process, the entire assay can be performed within an hour.

Light-Start CRISPR-Cas12a Reaction with Caged crRNA Enables Rapid and Sensitive Nucleic Acid Detection.

The clustered regularly interspaced short palindromic repeats (CRISPR) system is a promising platform for nucleic acid detection. Regulating the CRISPR reaction would be extremely useful to improve the detection efficiency and speed of CRISPR diagnostic applications. Here, we have developed a light-start CRISPR-Cas12a reaction by employing caged CRISPR RNA (crRNA). When combined with recombinase polymerase amplification, a robust photocontrolled one-pot assay is achieved. The photocontrolled one-pot assay is simpler and is 50-fold more sensitive than the conventional assay. This improved detection efficiency also facilitates the development of a faster CRISPR diagnostic method. The detection of clinical samples demonstrated that 10-20 min is sufficient for effective detection, which is much faster than the current gold-standard technique PCR. We expect this advance in CRISPR diagnostics to promote its widespread detection applications in biomedicine, agriculture, and food safety.

Synthesis, DFT and In Silico Anti-COVID Evaluation of Novel Tetrazole Analogues

A new series of 3-aryl/heteroaryl-2-(1H-tetrazol-5-yl) acrylamides have been synthesized through catalyst-free, one-pot cascade reactions, utilizing click chemistry approach and evaluated for their anti-COVID activities against two proteins in silico. The structural properties of the synthesized molecules were evaluated based on DFT calculations. Total energy of the synthesized tetrazole compounds were obtained through computational analysis which indicate the high stability of the synthesized compounds. The Frontier Molecular Orbitals (FMO) and associated energies and molecular electrostatic potential (MEP) surfaces were generated for the compounds. Spectral analysis by DFT gave additional evidence to the structural properties of the synthesized molecules. All tetrazole analogues come under good ADMET data as they followed the standard value for ADMET parameters. Docking studies offered evidence of the molecules displaying excellent biological properties as an anti-Covid drug. Compound 4 g exhibited excellent anti-COVID-19 properties with four hydrogen binding interactions with amino acids GLN 2.486 Å, GLN 2.436 Å, THR 2.186 Å and HSD 2.468 Å with good full-fitness score (–1189.12) and DeltaG (–7.19). Similarly, compound 4d shown potent activity against anti-COVID-19 mutant protein (PDB: 3K7H) with three hydrogen binding interactions, i.e., SER 2.274 Å, GLU 1.758 Å and GLU 1.853 Å with full-fitness score of –786.60) and DeltaG (–6.85). The result of these studies revealed that the compounds have the potential to become lead molecules in the drug discovery process.

CDetection.v2: One-pot assay for the detection of SARS-CoV-2.

Introduction: The ongoing 2019 coronavirus disease pandemic (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its variants, is a global public health threat. Early diagnosis and identification of SARS-CoV-2 and its variants plays a critical role in COVID-19 prevention and control. Currently, the most widely used technique to detect SARS-CoV-2 is quantitative reverse transcription real-time quantitative PCR (RT-qPCR), which takes nearly 1 hour and should be performed by experienced personnel to ensure the accuracy of results. Therefore, the development of a nucleic acid detection kit with higher sensitivity, faster detection and greater accuracy is important. Methods: Here, we optimized the system components and reaction conditions of our previous detection approach by using RT-RAA and Cas12b. Results: We developed a Cas12b-assisted one-pot detection platform (CDetection.v2) that allows rapid detection of SARS-CoV-2 in 30 minutes. This platform was able to detect up to 5,000 copies/ml of SARS-CoV-2 without cross-reactivity with other viruses. Moreover, the sensitivity of this CRISPR system was comparable to that of RT-qPCR when tested on 120 clinical samples. Discussion: The CDetection.v2 provides a novel one-pot detection approach based on the integration of RT-RAA and CRISPR/Cas12b for detecting SARS-CoV-2 and screening of large-scale clinical samples, offering a more efficient strategy for detecting various types of viruses.

Direct One-Pot Synthesis of Propofol from Paracetamol Tablets

The COVID-19 pandemic has affected millions of people in the entire world and caused a shortage of several drugs, including propofol. Therefore, several protocols for propofol synthesis have been published in recent years. Herein, we present a process starting from paracetamol, a very common and abundant active pharmaceutical ingredient. Since the first three steps (Friedel-Crafts double alkylation, acetyl deprotection, and diazotization) are done in acidic media, a one-pot approach was developed. Furthermore, we observed that the extraction of the final product can be simplified by steam-distillation, leading to propofol in 47% isolated yield with high purity. This presented process could be an example of active pharmaceutical ingredient reuse since similar results were observed with commercial paracetamol tablets (with excipients) regardless of expiration date. © 2023 American Chemical Society.

Progress and bioapplication of CRISPR-based one-step, quantitative and multiplexed infectious disease diagnostics.

In Vitro Diagnosis (IVD) technology is able to accurately detect pathogens or biomarkers at an initial stage of disease, which works as an important toolbox for disease diagnosis. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) system, as an emerging IVD method, plays a crucial role in the field of infectious disease detection due to its superior sensitivity and specificity. Recently, an increasing number of scientists have been devoted to improving the performance of CRISPR-based detection and on-site point-of-care testing (POCT) from extraction-free detection, amplification-free, modified Cas/crRNA complexes, quantitative assays, one-pot detection, and multiplexed platform. In this review, we describe the potential roles of these novel approaches and platforms in one-pot methods, quantitative molecular diagnostics as well as multiplexed detection. This review will not only help guide the full use of the CRISPR-Cas tools for quantification, multiplexed detection, POCT and as next-generation diagnostic biosensing platforms but also inspire new ideas, technological advances, and engineering strategies to address real-world challenges like the ongoing COVID-19 pandemic.

Light-Driven Catalyst-Free Access to Phthalazines: Entry to Antiviral Model Drugs by Merging Domino Reactions**

We report the development of a metal-free four-step one-pot synthetic strategy to access high-value functionalized phthalazines using o-methyl benzophenones as starting compounds. Combining a light-mediated enolization of o-methyl benzophenones/Diels-Alder reaction domino process with a subsequent deprotection/aromatization domino reaction in one-pot leads to sustainable and efficient organic synthesis. The tangible advantages, i. e., absence of catalysts or additives, utilization of commercially available and/or easily accessible substrates, mild reaction conditions, simplicity, and single work-up procedure, make this combined process highly appealing for the direct construction of various 1-aryl-phthalazines. Importantly, in vitro bioactivity evaluation of these newly prepared heterocyclic compounds demonstrated a strong antiviral efficacy against major human pathogens like HCMV and SARS-CoV-2. © 2022 The Authors. European Journal of Organic Chemistry published by Wiley-VCH GmbH.

In-situ fabrication of 3D interior hotspots templated with a protein@Au core-shell structure for label-free and on-site SERS detection of viral diseases

Nanoscale plasmonic hotspots play a critical role in the enhancement of molecular Raman signals, enabling the sensitive and reliable trace analysis of biomedical molecules via surface-enhanced Raman spectroscopy (SERS). However, effective and label-free SERS diagnoses in practical fields remain challenging because of clinical samples' random adsorption and size mismatch with the nanoscale hotspots. Herein, we suggest a novel SERS strategy for interior hotspots templated with protein@Au core-shell nanostructures prepared via electrochemical one-pot Au deposition. The cytochrome c and lysates of SARS-CoV-2 (SLs) embedded in the interior hotspots were successfully functionalized to confine the electric fields and generate their optical fingerprint signals, respectively. Highly linear quantitative sensitivity was observed with the limit-of-detection value of 10-1 PFU/ mL. The feasibility of detecting the targets in a bodily fluidic environment was also confirmed using the proposed templates with SLs in human saliva and nasopharyngeal swabs. These interior hotspots templated with the target analytes are highly desirable for early and on-site SERS diagnoses of infectious diseases without any labeling processes.

Direct One-Pot Synthesis of Propofol from Paracetamol Tablets

The COVID-19 pandemic has affected millions of people in the entire world and caused a shortage of several drugs, including propofol. Therefore, several protocols for propofol synthesis have been published in recent years. Herein, we present a process starting from paracetamol, a very common and abundant active pharmaceutical ingredient. Since the first three steps (Friedel-Crafts double alkylation, acetyl deprotection, and diazotization) are done in acidic media, a one-pot approach was developed. Furthermore, we observed that the extraction of the final product can be simplified by steam-distillation, leading to propofol in 47% isolated yield with high purity. This presented process could be an example of active pharmaceutical ingredient reuse since similar results were observed with commercial paracetamol tablets (with excipients) regardless of expiration date. © 2023 American Chemical Society.

Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3-d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro.

In this paper, an environmentally benign, convenient, and efficient one-pot three-component reaction has been developed for the regioselective synthesis of novel 5-aroyl(or heteroaroyl)-6-(alkylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-diones (4a‒n) through the sequential condensation of aryl(or heteroaryl)glyoxal monohydrates (1a‒g), 1,3-dimethylbarbituric acid (2), and alkyl(viz. cyclohexyl or tert-butyl)isocyanides (3a or 3b) catalyzed by ultra-low loading ZrOCl2•8H2O (just 2 mol%) in water at 50 ˚C. After synthesis and characterization of the mentioned furo[2,3-d]pyrimidines (4a‒n), their multi-targeting inhibitory properties were investigated against the active site and putative allosteric hotspots of both SARS-CoV-2 main protease (MPro) and papain-like protease (PLPro) based on molecular docking studies and compare the attained results with various medicinal compounds which approximately in three past years were used, introduced, and or repurposed to fight against COVID-19. Furthermore, drug-likeness properties of the mentioned small heterocyclic frameworks (4a‒n) have been explored using in silico ADMET analyses. Interestingly, the molecular docking studies and ADMET-related data revealed that the novel series of furo[2,3-d]pyrimidines (4a‒n), especially 5-(3,4-methylendioxybenzoyl)-6-(cyclohexylamino)-1,3-dimethylfuro[2,3-d]pyrimidine-2,4(1H,3H)-dione (4g) as hit one is potential COVID-19 drug candidate, can subject to further in vitro and in vivo studies. It is worthwhile to note that the protein-ligand-type molecular docking studies on the human body temperature-dependent MPro protein that surprisingly contains zincII (ZnII) ion between His41/Cys145 catalytic dyad in the active site, which undoubtedly can make new plans for designing novel SARS-CoV-2 MPro inhibitors, is performed for the first time in this paper, to the best of our knowledge.

Light‐Driven Catalyst‐Free Access to Phthalazines: Entry to Antiviral Model Drugs by Merging Domino Reactions**

We report the development of a metal-free four-step one-pot synthetic strategy to access high-value functionalized phthalazines using o-methyl benzophenones as starting compounds. Combining a light-mediated enolization of o-methyl benzophenones/Diels-Alder reaction domino process with a subsequent deprotection/aromatization domino reaction in one-pot leads to sustainable and efficient organic synthesis. The tangible advantages, i. e., absence of catalysts or additives, utilization of commercially available and/or easily accessible substrates, mild reaction conditions, simplicity, and single work-up procedure, make this combined process highly appealing for the direct construction of various 1-aryl-phthalazines. Importantly, in vitro bioactivity evaluation of these newly prepared heterocyclic compounds demonstrated a strong antiviral efficacy against major human pathogens like HCMV and SARS-CoV-2.

In-situ fabrication of 3D interior hotspots templated with a protein@Au core–shell structure for label-free and on-site SERS detection of viral diseases

Nanoscale plasmonic hotspots play a critical role in the enhancement of molecular Raman signals, enabling the sensitive and reliable trace analysis of biomedical molecules via surface-enhanced Raman spectroscopy (SERS). However, effective and label-free SERS diagnoses in practical fields remain challenging because of clinical samples' random adsorption and size mismatch with the nanoscale hotspots. Herein, we suggest a novel SERS strategy for interior hotspots templated with protein@Au core–shell nanostructures prepared via electrochemical one-pot Au deposition. The cytochrome c and lysates of SARS-CoV-2 (SLs) embedded in the interior hotspots were successfully functionalized to confine the electric fields and generate their optical fingerprint signals, respectively. Highly linear quantitative sensitivity was observed with the limit-of-detection value of 10−1 PFU/mL. The feasibility of detecting the targets in a bodily fluidic environment was also confirmed using the proposed templates with SLs in human saliva and nasopharyngeal swabs. These interior hotspots templated with the target analytes are highly desirable for early and on-site SERS diagnoses of infectious diseases without any labeling processes.

Light‐Driven Catalyst‐Free Access to Phthalazines: Entry to Antiviral Model Drugs by Merging Domino Reactions****A previous version of this manuscript has been deposited on a preprint server (https://doi.org/10.26434/chemrxiv‐2022‐j4xvz)

We report the development of a metal‐free four‐step one‐pot synthetic strategy to access high‐value functionalized phthalazines using o‐methyl benzophenones as starting compounds. Combining a light‐mediated enolization of o‐methyl benzophenones/Diels‐Alder reaction domino process with a subsequent deprotection/aromatization domino reaction in one‐pot leads to sustainable and efficient organic synthesis. The tangible advantages, i. e., absence of catalysts or additives, utilization of commercially available and/or easily accessible substrates, mild reaction conditions, simplicity, and single work‐up procedure, make this combined process highly appealing for the direct construction of various 1‐aryl‐phthalazines. Importantly, in vitro bioactivity evaluation of these newly prepared heterocyclic compounds demonstrated a strong antiviral efficacy against major human pathogens like HCMV and SARS‐CoV‐2.

One-pot synthesis, molecular docking, ADMET, and DFT studies of novel pyrazolines as promising SARS-CoV-2 main protease inhibitors

Pyrazoline and its derivatives have numerous prominent pharmacological effects. Focusing on its anti-viral property, we have designed and synthesized three novel pyrazoline derivatives (A1–A3) through one-pot three components and characterized them using different spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, and UV). These compounds were evaluated against SARS-CoV-2 main protease utilizing in-silico molecular docking studies. The docking results displayed good inhibitory activity of the synthesized compounds. Among them, compound A2 was the most active against targeted protein. The drug-likeness and ADMET properties were predicted to have varied profiles but could still be developed, especially A2. DFT/TD-DFT calculations through B3LYP/6-311G++ level of theory were applied to provide comparable theoretical data along with MEP map and electronic energy gap of HOMO → LUMO. [ FROM AUTHOR] Copyright of Research on Chemical Intermediates is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Disposable and low-cost pen-like sensor incorporating nucleic-acid amplification based lateral-flow assay for at-home tests of communicable pathogens.

Rapid at-home test is a good alternative to the gold standard quantitative polymerase chain reaction (qPCR) for early identification and management of infected individuals in pandemic. However, the currently available at-home rapid antigen kits and nucleic acid tests (NATs) are prone to false results. Although some CRISPR-mediated NATs enhanced accuracy, long turnaround time (ca. 1 h) and aerosol contamination due to additional open-lid reaction hinder its applicability for self-tests. Moreover, the accuracy of at-home NATs is also impacted by interference of sample matrix due to lack of sample purification. Here we report a Fast, Low-cost, Aerosol contamination-free and Sensitive molecular assay for at-Home tests of communicable pathogens (FLASH) incorporating oLAMP, a recently reported isothermal and target-specific NATs by our group, and a visible lateral-flow readout. The integrated platform enabled sample-to-result SARS-CoV-2 RNA detection in 20-30 min achieving a sensitivity of 0.5 copies/µL in a blinded experiment with a high accuracy comparable with the qPCR. Its prototype consists of two disposable pen-like instruments for single-step sample preparation and contamination-free NATs, respectively. The simplified workflow of the FLASH enabled detection to be readily conducted by untrained users for at-home tests. All in all, the FLASH prototype demonstrates itself to be a promising home-use assay platform for effective mitigation of the pandemic.

Advances in Synthetic Strategies and Medicinal Importance of Benzofurans: A Review

Out of the many heterocycles that exhibit pharmaceutical and therapeutic properties, benzofurans remain the most eye-catching to scientists ever since their discovery. From being present in natural products to synthetic analogs they show diverse biological properties which are used to treat various diseases. Interestingly, some of the benzofuran hybrids were docked against COVID-19 Main Protease and it showed appealing results. Apart from medicinal properties it also exhibits some non-drug applications. The structure activity relationship of benzofuran derivatives in many infections draws attention to the extent where drugs can be produced in a short time span which highlights their significance in medicinal chemistry. There are considerable reaction schemes to synthesize this moiety either simple one pot reactions or multistep. Here, we emphasize on the chemistry of benzofurans, synthesis and its derivatives in the recent years, some of which show notable anti-tumor, anti-fungal, anti-mycobacterial and anti-oxidant activities.

New Phosphinic and Phosphonic acids: Synthesis, antidiabetic, anti-Alzheimer, antioxidant activity, DFT study and SARS-CoV-2 inhibition

Two new α-aminophosphinic (A) and α-aminophosphonic (B) acids were synthesized through a one-pot three-component reaction with good yields of 89 % and 85 %, respectively. The NMR and mass spectroscopies have been used to identify the obtained compounds and confirm their structures, while the IR spectroscopy has been used to characterize functional groups and the type of vibrations involved for the studied compounds. Moreover, the examination of the structural properties and the comparison between the theoretical and the experimental results have been performed using DFT/B3LYP/6-31G (d,p) method. Consequently, the calculated values of the total energy and the energy gap indicate that the (B) is more stable and less reactive than the (A). Also, MEP maps show that oxygen atoms are the probable sites of electrophilic reactions. In this context, the high reactivity of the (A) can be related to the replacement of the (OH) functional group by a hydrogen atom. Further, six in vitro assays have been used to evaluate the antioxidant potential of (A) and (B), which illustrate that both compounds exhibited an excellent activity (e.g., DPPH/IC50(B): 2.42 μg/mL and DPPH/IC50(A): 2.10 μg /mL). The anti-Alzheimer and antidiabetic effects of the studied compounds have been estimated in vitro by evaluating their inhibition of acetylcholinesterase, butyrylcholinesterase and α-glucosidase. The both compounds showed a good inhibitory activity for α-glucosidase (IC50(A): 12.63 and IC50(B): 25.26 μg/mL), and exhibited higher inhibitory activity against butyrylcholinesterase (BChE) than against acetylcholinesterase (AChE) (IC50(A): 36.71±0.95 and IC50(B): 26.56±1.32 μg/mL). Furthermore, the in silico docking study of the inhibitory action of SARS-CoV-2 main protease (Mpro) showed that (A) and (B) have a significant inhibitory action with total energy values of - 96.23 and - 99.99 kcal/mol, respectively.

Photocontrolled crRNA activation enables robust CRISPR-Cas12a diagnostics.

CRISPR diagnostics based on nucleic acid amplification faces barriers to its commercial use, such as contamination risks and insufficient sensitivity. Here, we propose a robust solution involving optochemical control of CRISPR RNA (crRNA) activation in CRISPR detection. Based on this strategy, recombinase polymerase amplification (RPA) and CRISPR-Cas12a detection systems can be integrated into a completely closed test tube. crRNA can be designed to be temporarily inactivated so that RPA is not affected by Cas12a cleavage. After the RPA reaction is completed, the CRISPR-Cas12a detection system is activated under rapid light irradiation. This photocontrolled, fully closed CRISPR diagnostic system avoids contamination risks and exhibits a more than two orders of magnitude improvement in sensitivity compared with the conventional one-pot assay. This photocontrolled CRISPR method was applied to the clinical detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, achieving detection sensitivity and specificity comparable to those of PCR. Furthermore, a compact and automatic photocontrolled CRISPR detection device was constructed.

One-Pot Consecutive Reductive Amination Synthesis of Pharmaceuticals: From Biobased Glycolaldehyde to Hydroxychloroquine

Reductive amination plays a paramount role in the synthesis of amines. It is often proposed as a more ecofriendly synthesis process than the traditional SN2-type reactions of amines as it avoids toxic alkylation reagents such as alkyl halides. This work demonstrates the versatility of the reductive amination reaction via the synthesis of hydroxychloroquine (HCQ), one of the most renowned pharmaceuticals during this coronavirus pandemic. The novel green synthesis strategy is based on three consecutive reductive amination reactions conducted in a one-pot system, avoiding intermediary purification steps. Furthermore, a biobased C2 platform molecule, glycolaldehyde, was selected as a starting reagent. The newly developed reductive amination pathway was appraised using the CHEM21 Green Metric toolkit and compared with the commercially operating method. © 2022 American Chemical Society.

Rational Design of CRISPR/Cas12a-RPA Based One-Pot COVID-19 Detection with Design of Experiments.

Simple and effective molecular diagnostic methods have gained importance due to the devastating effects of the COVID-19 pandemic. Various isothermal one-pot COVID-19 detection methods have been proposed as favorable alternatives to standard RT-qPCR methods as they do not require sophisticated and/or expensive devices. However, as one-pot reactions are highly complex with a large number of variables, determining the optimum conditions to maximize sensitivity while minimizing diagnostic cost can be cumbersome. Here, statistical design of experiments (DoE) was employed to accelerate the development and optimization of a CRISPR/Cas12a-RPA-based one-pot detection method for the first time. Using a definitive screening design, factors with a significant effect on performance were elucidated and optimized, facilitating the detection of two copies/µL of full-length SARS-CoV-2 (COVID-19) genome using simple instrumentation. The screening revealed that the addition of a reverse transcription buffer and an RNase inhibitor, components generally omitted in one-pot reactions, improved performance significantly, and optimization of reverse transcription had a critical impact on the method's sensitivity. This strategic method was also applied in a second approach involving a DNA sequence of the N gene from the COVID-19 genome. The slight differences in optimal conditions for the methods using RNA and DNA templates highlight the importance of reaction-specific optimization in ensuring robust and efficient diagnostic performance. The proposed detection method is automation-compatible, rendering it suitable for high-throughput testing. This study demonstrated the benefits of DoE for the optimization of complex one-pot molecular diagnostics methods to increase detection sensitivity.