Sona Lyndem

Bio: Sona Lyndem is an academic researcher from National Institute of Technology, Meghalaya. The author has contributed to research in topics: Chemistry & Quenching (fluorescence). The author has an hindex of 1, co-authored 2 publications receiving 175 citations.

An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study.

Abstract: A new strain of a novel infectious disease affecting millions of people, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently been declared as a pandemic by the World...

Interaction Properties of Biosynthesized Cadmium Sulphide Quantum Dots with Human Serum Albumin: Further Investigation of Antibacterial Activities and Sensing Applications.

Abstract: Synthesis of low dimensional quantum dots (QDs) (1-10 nm) via green route has garnered great interest having the prospective use in many biological applications (diagnosis, drug delivery and in vivo sensing), which is difficult to achieve by chemical synthesize methods having larger QDs particles or hazardous reagents required for synthesizing of QDs. Here, we have synthesized biogenic cadmium sulphide (CdS) QDs using green tea extract as reducing agents that were homogeneous and smaller size particles 2-4 nm. We also elucidate the (a) protein binding, (b) antibacterial and (c) sensing applications of biogenic CdS QDs in this present work. The biosynthesized CdS QDs were found to have extensive antibacterial activity against both gram-negative E. coli and gram-positive E. faecalis bacterial strains. Since the introduction of QDs in biological media, they can form protein-QDs complex; hence we investigate the binding interaction of CdS QDs with the carrier protein human serum albumin (HSA) in vitro. The synthesized CdS QDs quenched the intrinsic fluorescence of HSA through static quenching mechanism and binding constant (Kb ) was found in order of 104 M-1 . It was also observed that presence of biogenic CdS QDs affects the HSA-ligand interactions in vitro. The synthesized CdS showed highly effective sensors for tetracycline, rifampicin and bilirubin with LOD values of 99, 141 and 29 ng/mL respectively.

A comprehensive in vitro exploration into the interaction mechanism of coumarin derivatives with bovine hemoglobin: Spectroscopic and computational methods

Abstract: • Binding of coumarin derivatives with bovine hemoglobin have been investigated using biophysical techniques. • Static quenching mechanism is involved in the binding interactions of coumarins with bovine hemoglobin. • Binding constant was found moderate in nature. • Secondary structure of the protein was perturbed during ligand binding. • Results from computational studies correlated well with the experimental findings. Biological functioning takes place through the interaction of biomacromolecules with each other or with other small molecules. The molecular recognition of a carrier protein, bovine hemoglobin (BHb), with 7-hydroxycoumarin (7-HC) and 4-methyl-7-hydroxycoumarin (4-Me-7-HC) was investigated using various biophysical and computational techniques. Fluorescence spectroscopy and molecular docking revealed the interaction of 7-HC and 4-Me-7-HC with β 2 -Trp37 fluorophore, quenching the intrinsic fluorescence of BHb. The mechanism of quenching was determined to be static. The binding constant ( K b ) for BHb with 7-HC and 4-Me-7-HC was found to be 6.15×10 4 M -1 and 5.73 ×10 4 M -1 at 298 K, respectively. This moderate form of protein-ligand association could result in reversible binding to transport and release the ligand in the target tissue. Negative Δ G for both complexes suggested spontaneous binding. Positive Δ H and Δ S for BHb-7-HC indicated hydrophobic forces played a dominant role in binding. However, hydrogen bonding and hydrophobic forces dictated the binding process for BHb-4-Me-7-HC due to obtaining negative Δ H and positive Δ S values. Changes in the microenvironment of the binding site were observed through 3D fluorescence studies. Through Förster resonance energy transfer (FRET), a binding distance of less than 7 nm was measured between BHb and7-HC/4-Me-7-HC. The interaction of coumarin derivatives with BHb resulted in a loss of α-helical content of the protein, as proven by circular dichroism (CD) and Fourier transform infrared (FTIR) measurements. Molecular dynamic simulations showed the binding of 7-HC supplemented the stability of BHb, whereas 4-Me-7-HC binding resulted in conformational changes in the structure of BHb.

Molecular recognition of two bioactive coumarin derivatives 7-hydroxycoumarin and 4-methyl-7-hydroxycoumarin by hen egg white lysozyme: Exploring the binding mechanism, thermodynamic parameters and structural changes using multispectroscopic and computational approaches.

Abstract: Multispectroscopic and computational methods of exploring the interaction between a carrier protein and therapeutic compounds provide a preliminary investigation into establishing the efficacy of s...

Using X-ray images and deep learning for automated detection of coronavirus disease.

Abstract: Coronavirus is still the leading cause of death worldwide. There are a set number of COVID-19 test units accessible in emergency clinics because of the expanding cases daily. Therefore, it is important to implement an automatic detection and classification system as a speedy elective finding choice to forestall COVID-19 spreading among individuals. Medical images analysis is one of the most promising research areas, it provides facilities for diagnosis and making decisions of a number of diseases such as Coronavirus. This paper conducts a comparative study of the use of the recent deep learning models (VGG16, VGG19, DenseNet201, Inception_ResNet_V2, Inception_V3, Resnet50, and MobileNet_V2) to deal with detection and classification of coronavirus pneumonia. The experiments were conducted using chest X-ray & CT dataset of 6087 images (2780 images of bacterial pneumonia, 1493 of coronavirus, 231 of Covid19, and 1583 normal) and confusion matrices are used to evaluate model performances. Results found out that the use of inception_Resnet_V2 and Densnet201 provide better results compared to other models used in this work (92.18% accuracy for Inception-ResNetV2 and 88.09% accuracy for Densnet201).Communicated by Ramaswamy H. Sarma.

Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors - an in silico docking and molecular dynamics simulation study.

Abstract: Coronavirus disease 2019 (COVID-19) is a viral respiratory disease which caused global health emergency and announced as pandemic disease by World Health Organization Lack of specific drug molecul

Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in silico study for drug development.

Abstract: Spike glycoprotein, a class I fusion protein harboring the surface of SARS-CoV-2 (SARS-CoV-2S), plays a seminal role in the viral infection starting from recognition of the host cell surface receptor, attachment to the fusion of the viral envelope with the host cells. Spike glycoprotein engages host Angiotensin-converting enzyme 2 (ACE2) receptors for entry into host cells, where the receptor recognition and attachment of spike glycoprotein to the ACE2 receptors is a prerequisite step and key determinant of the host cell and tissue tropism. Binding of spike glycoprotein to the ACE2 receptor triggers a cascade of structural transitions, including transition from a metastable pre-fusion to a post-fusion form, thereby allowing membrane fusion and internalization of the virus. From ancient times people have relied on naturally occurring substances like phytochemicals to fight against diseases and infection. Among these phytochemicals, flavonoids and non-flavonoids have been the active sources of different anti-microbial agents. We performed molecular docking studies using 10 potential naturally occurring compounds (flavonoids/non-flavonoids) against the SARS-CoV-2 spike protein and compared their affinity with an FDA approved repurposed drug hydroxychloroquine (HCQ). Further, our molecular dynamics (MD) simulation and energy landscape studies with fisetin, quercetin, and kamferol revealed that these molecules bind with the hACE2-S complex with low binding free energy. The study provided an indication that these molecules might have the potential to perturb the binding of hACE2-S complex. In addition, ADME analysis also suggested that these molecules consist of drug-likeness property, which may be further explored as anti-SARS-CoV-2 agents. Communicated by Ramaswamy H. Sarma.

Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

Abstract: The pandemic caused by novel coronavirus disease 2019 (COVID-19) infecting millions of populations worldwide and counting, has demanded quick and potential therapeutic strategies. Current approved drugs or molecules under clinical trials can be a good pool for repurposing through in-silico techniques to quickly identify promising drug candidates. The structural information of recently released crystal structures of main protease (Mpro) in APO and complex with inhibitors, N3, and 13b molecules was utilized to explore the binding site architecture through Molecular dynamics (MD) simulations. The stable state of Mpro was used to conduct extensive virtual screening of the aforementioned drug pool. Considering the recent success of HIV protease molecules, we also used anti-protease molecules for drug repurposing purposes. The identified top hits were further evaluated through MD simulations followed by the binding free energy calculations using MM-GBSA. Interestingly, in our screening, several promising drugs stand out as potential inhibitors of Mpro. However, based on control (N3 and 13b), we have identified six potential molecules, Leupeptin Hemisulphate, Pepstatin A, Nelfinavir, Birinapant, Lypression and Octreotide which have shown the reasonably significant MM-GBSA score. Further insight shows that the molecules form stable interactions with hot-spot residues, that are mainly conserved and can be targeted for structure- and pharmacophore-based designing. The pharmacokinetic annotations and therapeutic importance have suggested that these molecules possess drug-like properties and pave their way for in-vitro studies.Communicated by Ramaswamy H. Sarma.

Identification of phytochemical inhibitors against main protease of COVID-19 using molecular modeling approaches.

Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a novel corona virus that causes corona virus disease 2019 (COVID-19). The COVID-19 rapidly spread across the nations with high mortality rate even as very little is known to contain the virus at present. In the current study, we report novel natural metabolites namely, ursolic acid, carvacrol and oleanolic acid as the potential inhibitors against main protease (Mpro) of COVID-19 by using integrated molecular modeling approaches. From a combination of molecular docking and molecular dynamic (MD) simulations, we found three ligands bound to protease during 50 ns of MD simulations. Furthermore, the molecular mechanic/generalized/Born/Poisson-Boltzmann surface area (MM/G/P/BSA) free energy calculations showed that these chemical molecules have stable and favourable energies causing strong binding with binding site of Mpro protein. All these three molecules, namely, ursolic acid, carvacrol and oleanolic acid, have passed the ADME (Absorption, Distribution, Metabolism, and Excretion) property as well as Lipinski's rule of five. The study provides a basic foundation and suggests that the three phytochemicals, viz. ursolic acid, carvacrol and oleanolic acid could serve as potential inhibitors in regulating the Mpro protein's function and controlling viral replication. Communicated by Ramaswamy H. Sarma.