Molecular dynamics simulations of the delta and omicron SARS-CoV-2 spike – ACE2 complexes reveal distinct changes between both variants

SARS-CoV-2, the virus which causes the COVID-19 pandemic, changes frequently through the ap-pearance of mutations constantly leading to new variants. However, only few variants evolve as dominating and will be considered as “Variants of Concern” (VOCs) by the world health organization (WHO). At the end of 2020 the alpha (B.1.1.7) variant appeared in the United Kingdom and domi-nated the pandemic situation until mid of 2021 when it was substituted by the delta variant (B.1.617.2) that first appeared in India as predominant variant. At the end of 2021, SARS-CoV-2 omi-cron (B.1.1.529) evolved as the dominating variant. Here, we use in silico modeling and molecular dynamics (MD) simulations of the receptor-binding domain of the viral spike protein and the host cell surface receptor ACE2 to analyze and compare the interaction pattern between the wild type, delta and omicron variants. We identified residue 493 in delta (glutamine) and omicron (arginine) with altered binding properties towards ACE2.

Modeling the technology of identification of wine materials and wines by PCR analysis of microsatellite loci of grapevine chloroplast DNA

Использование полиморфных микросателлитных локусов ДНК является одним из подходов к аутентификации виноматериалов и вин. При этом SSR-маркеры хлоропластной ДНК имеют большую копийность мишени на клетку и менее подвержены деградации из-за содержания в органеллах с двойной мембраной. Целью настоящей работы являлось моделирование технологии идентификации виноматериалов и вин ПЦР-анализом микросателлитных локусов хлоропластной ДНК винограда. Подобраны условия экстракции нуклеиновых кислот, постановки ПЦР с соответствующими наборами праймеров и электрофоретической детекции, направленные на практическое воспроизведение генетического тестирования пробоподготовленного биоматериала из осаждаемого винного дебриса. Представлены наглядные результаты выравнивания частичных нуклеотидных последовательностей аллелей микросателлитных локусов хлоропластной ДНК Vitis vinifera L. Проанализирована разделяющая способность метода горизонтального электрофореза в геле «Spreadex EL 300» in silico моделированием генерируемых аллельспецифичных фрагментов, позволяющая идентифицировать известные хлоротипы винограда даже при постановке ПЦР с ограниченными наборами праймеров, нацеленных на локусы cpSSR3, cpSSR5, cpSSR10, NTCP12 и ccSSR9. The use of polymorphic microsatellite DNA loci is one of the approaches to the authentication of wine materials and wines. At the same time, SSR markers of chloroplast DNA have a large target copy number per cell and are less susceptible to degradation due to their content in organelles with a double membrane. The aim of this work was to simulate the technology of identification of wine materials and wines by PCR analysis of microsatellite loci of grapevine chloroplast DNA. The conditions for the extraction of nucleic acids, PCR with the corresponding sets of primers and electrophoretic detection were selected, aimed at the practical reproduction of genetic testing of the sample prepared biomaterial from the precipitated wine debris. Illustrative results of the alignment of partial nucleotide sequences of alleles of microsatellite loci of Vitis vinifera L. chloroplast DNA are presented. The separating ability of the method of horizontal electrophoresis in «Spreadex EL 300» gel by in silico modeling the generated allele-specific fragments, which makes it possible to identify the known chlorotypes of grapevine with a limited set of primers targeting loci (cpSSR3, cpSSR5, cpSSR10, NTCP12 and ccSSR9) has been analyzed.

The TOG protein Stu2 is regulated by acetylation

Stu2 in S. cerevisiae is a member of the XMAP215/Dis1/Alp14/Msps/CKAP5/ch-TOG family of MAPs and has multiple functions in controlling microtubules, including microtubule polymerization, microtubule depolymerization, linking chromosomes to the kinetochore, and assembly of γ-TuSCs at the SPB. Whereas phosphorylation has been shown to be critical for Stu2 localization at the kinetochore, other regulatory mechanisms that control Stu2 function are still poorly understood. Here, we show that a novel form of Stu2 regulation occurs through the acetylation of three lysine residues at K252, K469, and K870, which are located in three distinct domains of Stu2. Alteration of acetylation through acetyl-mimetic and acetyl-blocking mutations did not impact the essential function of Stu2. Instead, these mutations lead to both positive and negative changes in chromosome stability, as well as changes in resistance to the microtubule depolymerization drug, benomyl. In agreement with our in silico modeling, several acetylation-mimetic mutants displayed increased interactions with γ-tubulin. Taken together, these data suggest that Stu2 acetylation can govern multiple Stu2 functions in both a positive and negative manner, including chromosome stability and interactions at the SPB.

in silico Modeling of Curcumin Based Sulfonamides Inhibitors of the Human trans-Membrane Carbonic Anhydrase Isozyme, hCA IX by CoMSIA

Carbonic anhydrases, hCAs IX and XII are applied as the markers of progression of the disease in many oxygen deficient tumours and their specially manoeuvred inhibition is directly related to containing the growth of both primary tumours and tumour growth of secondary nature. Ligand-based quantitative structure-activity relationship (QSAR) studies were carried out on curcumin related, sulphonamide derivatives as inhibitors of human trans-membrane carbonic anhydrase isozyme, hCA IX by comparative molecular field similarity analysis (CoMSIA) implemented through the SYBYL package. The capacity of the model to predict coveted compound was evaluated using test set of three compounds. The best model created was found to be of choice as it showed a r2 value of 0.811 and a cross validated coefficient q2 value of 0.617 in tripos CoMSIA hydrophobic region. Results of the present study indicated that hydrophobic region factors play an important role in carbonic anhydrase hCA IX inhibition for compounds.

In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses

Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce ubiquitination and subsequent degradation of proteins via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. Rational design of PROTACs requires accurate knowledge of the native configuration of the PROTAC induced ternary complex. This study demonstrates that native and non-native ternary complex poses can be distinguished based on pose occupancy time in MD, where native poses exhibit longer occupancy times than non-native ones at both room and higher temperatures. Candidate poses are generated by MD sampling and pre-ranked by the classic MM/GBSA method. A specific heating scheme is then applied to induce ternary pose departure, generating an occupancy score and temperature score reflecting pose occupancy time and fraction. The scoring approach enables identification of the native pose in all the test systems. Beyond providing a relative rank of hypothetical poses of a given ternary system, the method could also provide empirical guidance to whether a given ternary pose is likely a native one or not. The success of the method is in part attributed to the dynamic nature of the pose departure analysis which accounts for solute entropic effects, typically neglected in the faster static pose scoring methods, while solute entropic contributions play a greater role in protein-protein interactions than in protein-ligand systems.

The NSP14/NSP10 RNA repair complex as a Pan-coronavirus therapeutic target

The risk of zoonotic coronavirus spillover into the human population, as highlighted by the SARS-CoV-2 pandemic, demands the development of pan-coronavirus antivirals. The efficacy of existing antiviral ribonucleoside/ribonucleotide analogs, such as remdesivir, is decreased by the viral proofreading exonuclease NSP14-NSP10 complex. Here, using a novel assay and in silico modeling and screening, we identified NSP14-NSP10 inhibitors that increase remdesivir’s potency. A model compound, sofalcone, both inhibits the exonuclease activity of SARS-CoV-2, SARS-CoV, and MERS-CoV in vitro, and synergistically enhances the antiviral effect of remdesivir, suppressing the replication of SARS-CoV-2 and the related human coronavirus OC43. The validation of top hits from our primary screenings using cellular systems provides proof-of-concept for the NSP14 complex as a therapeutic target.