L-Type Calcium Channels: Structure and Functions

Voltage-gated calcium channels (VGCCs) manage the electrical signaling of cells by allowing the selective-diffusion of calcium ions in response to the changes in the cellular membrane potential. Among the different VGCCs, the long-lasting or the L-type calcium channels (LTCCs) are prevalently expressed in a variety of cells, such as skeletal muscle, ventricular myocytes, smooth muscles and dendritic cells and forms the largest family of the VGCCs. Their wide expression pattern and significant role in diverse cellular events, including neurotransmission, cell cycle, muscular contraction, cardiac action potential and gene expression, has made these channels the major targets for drug development. In this book chapter, we aim to provide a comprehensive overview of the different VGCCs and focus on the sequence-structure–function properties of the LTCCs. Our chapter will summarize and review the various experimental and computational analyses performed on the structures of the LTCCs and their implications in drug discovery applications

Reverse engineering: transaminase biocatalystdevelopment using ancestral sequencereconstruction

The development of new biocatalysts using ancestral sequence reconstruction is reported. When applied to an ω-transaminase, the ancestral proteins demonstrated novel and superior activities with eighty percent of the forty compounds tested compared to the modern day protein, and improvements in activity of up to twenty fold. These included a range of compounds pertinent as feedstocks in polyamide manufacture.MW and SK were supported by CSIRO Research Office Postdoctoral Fellowships

A minimum reporting standard for multiple sequence alignments

Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.CSIRO

Structure and ligand-based investigation of histone deacetylases towards cancer drug discovery

Submission note: A thesis submitted in complete fulfilment of the requirements for the degree of Doctor of Philosophy to the Department of Computer Science and Computer Engineering, School of Engineering and Mathematical Sciences, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora

Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations

Molecular channel exploration perseveres to be the prominent solution for eliciting structure and accessibility of active site and other internal spaces of macromolecules. The volume and silhouette characterization of these channels provides answers for the issues of substrate access and ligand swapping between the obscured active site and the exterior of the protein. Histone deacetylases (HDACs) are metal-dependent enzymes that are involved in the cell growth, cell cycle regulation, and progression, and their deregulations have been linked with different types of cancers. Hence HDACs, especially the class I family, are widely recognized as the important cancer targets, and the characterizations of their structures and functions have been of special interest in cancer drug discovery. The class I HDACs are known to possess two different protein channels, an 11 Å and a 14 Å (named channels A and B1, respectively), of which the former is a ligand or substrate occupying tunnel that leads to the buried active site zinc ion and the latter is speculated to be involved in product release. In this work, we have carried out random acceleration molecular dynamics (RAMD) simulations coupled with the classical molecular dynamics to explore the release of the ligand, <i>N</i>-(2-aminophenyl) benzamide (LLX) from the active sites of the recently solved X-ray crystal structure of HDAC2 and the computationally modeled HDAC1 proteins. The RAMD simulations identified significant structural and dynamic features of the HDAC channels, especially the key ‘gate-keeping’ amino acid residues that control these channels and the ligand release events. Further, this study identified a novel and unique channel B2, a subchannel from channel B1, in the HDAC1 protein structure. The roles of water molecules in the LLX release from the HDAC1 and HDAC2 enzymes are also discussed. Such structural and dynamic properties of the HDAC protein channels that govern the ligand escape reactions will provide further mechanistic insights into the HDAC enzymes, which, in the long run, have a potential to bring new ideas for developing more promising HDAC inhibitors as well as extend our atomic level understandings on their mechanisms of action

ModelFinder: fast model selection for accurate phylogenetic estimates

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space. Model-based molecular phylogenetic analysis plays a key role in comparative genomics and evolutionary biology, allowing us to annotate genomes more accurately1, test our understanding of the evolution of species, genomes and genes2–6, and determine the likely origins and routes of dispersal of pathogens and pests7,8. Selecting an optimal model of sequence evolution (SE) is a critical step in all such analyses. Here we introduce ModelFinder, a model-selection method that combines substitution models used in other popular model-selection methods9,10 with a flexible rate-heterogeneity-across-sites (RHAS

The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease

Abstract The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro’s susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of an Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrate a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild type enzyme. We show that other point mutations also significantly shift the equilibrium towards this state by altering conformational free energies. Unique avenues of SARS-CoV-2 research can be explored by understanding how H163 modulates this equilibrium

Design and Development of COX-II Inhibitors: Current Scenario and Future Perspective

Funding Information: Sandhya Chahal would like to thank CCS HAU for financial assistance in the form of a University Research Scholarship. Payal Rani and Kiran would like to thank UGC for financial assistance in the form of a Senior Research Fellowship. Gaurav Joshi would like to thank Department of Biotechnology, New Delhi, India (Grant No. BT/PR47642/CMD/150/24/2023) for work in the area of COX inhibitors development. Publisher Copyright: © 2023 The Authors. Published by American Chemical Society.Innate inflammation beyond a threshold is a significant problem involved in cardiovascular diseases, cancer, and many other chronic conditions. Cyclooxygenase (COX) enzymes are key inflammatory markers as they catalyze prostaglandins production and are crucial for inflammation processes. While COX-I is constitutively expressed and is generally involved in “housekeeping” roles, the expression of the COX-II isoform is induced by the stimulation of different inflammatory cytokines and also promotes the further generation of pro-inflammatory cytokines and chemokines, which affect the prognosis of various diseases. Hence, COX-II is considered an important therapeutic target for drug development against inflammation-related illnesses. Several selective COX-II inhibitors with safe gastric safety profiles features that do not cause gastrointestinal complications associated with classic anti-inflammatory drugs have been developed. Nevertheless, there is mounting evidence of cardiovascular side effects from COX-II inhibitors that resulted in the withdrawal of market-approved anti-COX-II drugs. This necessitates the development of COX-II inhibitors that not only exhibit inhibit potency but also are free of side effects. Probing the scaffold diversity of known inhibitors is vital to achieving this goal. A systematic review and discussion on the scaffold diversity of COX inhibitors are still limited. To address this gap, herein we present an overview of chemical structures and inhibitory activity of different scaffolds of known COX-II inhibitors. The insights from this article could be helpful in seeding the development of next-generation COX-II inhibitors.Peer reviewe