Parisa Amani - Academia.edu (original) (raw)

Papers by Parisa Amani

Journal of Molecular Liquids

ACS Chemical Neuroscience, 2021

Chemoinformatics appraisal and molecular docking were employed to investigate 225 complexes of 75... more Chemoinformatics appraisal and molecular docking were employed to investigate 225 complexes of 75 schizophrenia antipsychotics with the dopamine receptor subtypes D2R, D3R, and D4R. Considering the effective noncovalent interactions in the subtype-D2 receptor selectivity of antipsychotics, this study evaluated the possible physicochemical properties of ligands underlying the design of safer and more effective antipsychotics. The pan-assay interference compounds (PAINs) include about 25% of typical antipsychotics and 5% of atypicals. Popular antipsychotics like haloperidol, clozapine, risperidone, and aripiprazole are not PAINs. They have stronger interactions with D2R and D4R, but their interactions with D3R are slightly weaker, which is similar to the behavior of dopamine. In contrast to typical antipsychotics, atypical antipsychotics exhibit more noncovalent interactions with D4R than with D2R. These results suggest that selectivity to D2R and D4R comes from the synergy between hydrophobic and hydrogen-bonding interactions through their concomitant occurrence in the form of a hydrogen-bonding site adorned with hydrophobic contacts in antipsychotic-receptor complexes. All the antipsychotics had more synergic interactions with D2R and D4R in comparison with D3R. The atypical antipsychotics made a good distinction between the subtype D2 receptors with high selectivity to D4R. Among the popular antipsychotics, haloperidol, clozapine, and risperidone have hydrophobic-hydrogen-bonding synergy with D4R, while aripiprazole profits with D2R. The most important residue participating in the synergic interactions was threonine for D2R and cysteine for D4R. This work could be useful in informing and guiding future drug discovery and development studies aimed at receptor-specific antipsychotics.

Additional file 1: The software manual accompanies this paper as supplementary information.

Physical Chemistry Research, 2019

AChE is an enzyme that is predominate in a healthy brain, while BChE is considered to play a mino... more AChE is an enzyme that is predominate in a healthy brain, while BChE is considered to play a minor role in regulating the levels of ACh (memory molecule) in the brain. In addition to setting the ACh level, these two enzymes also facilitate Aβ aggregation by forming stable complexes and participate in the abnormal phosphorylation of the tau protein, which also contribute to the development of Alzheimer’s disease (AD). Trace elements including Zn2+, Cu2+, and Fe2+ are found in the brain plaques of Alzheimer’s patients. This study employed tacrine as an efficient inhibitor of cholinesterase and quercetin as a natural metal chelating agent to design a new multi-target-directed ligand, which has been named Tac-Quer. The chelating properties of this ligand have been studied by quantum calculations. The Tac-Quer/Metal binding energies for Zn2+, Cu2+, and Fe2+ are -939. 08, -917.62, and - 694.103 kcal.mol-1, respectively. The cholinesterase enzyme inhibitory activity of the Tac-Quer ligand ...

Applied Surface Science, 2020

The gas-adsorption behaviors of O 2 and H 2 on penta-graphene (PG) and Pt single atom@penta-graph... more The gas-adsorption behaviors of O 2 and H 2 on penta-graphene (PG) and Pt single atom@penta-graphene (Pt-PG) were investigated using density functional theory calculations. To illustrate the importance of the van der Waals (vdW) interactions, in addition to popular local density approximation (LDA) and semilocal Perdew-Burke-Ernzerhof generalized gradient approximation (GGA-PBEsol) functionals, two non-local (vdW-DF2 and rev-vdW-DF2) functionals were investigated through the correlation between energetic, structural, and electronic properties. On the surface of the PG (band gap 2.3 eV), O 2 was strongly physisorbed, which reduced the O 2 /PG band gap to~0.75 eV and created a p-type semiconductor. The H 2 was very weakly physisorbed without any changes in the band gap. On the semimetal Pt-PG (zero band gap), the H 2 and O 2 were strongly chemisorbed which was dissociative for H 2. H 2 adsorption opens a band gap of 1.45 eV, making the H 2 /Pt-PG system a semiconductor. But the O 2 /Pt-PG system remains semimetal. The PG can be used for the detection of O 2 but not for H 2. The presence of the Pt atoms allows the Pt-PG system to detect the H 2 very well. LDA is suggested for investigating H 2 adsorption on both the PG and Pt-PG systems, but the non-local vdWs must be used for the O 2 adsorption study.

Biotechnology Advances, 2015

Parasitic worm proteins that belong to the cysteine-rich secretory proteins, antigen 5 and pathog... more Parasitic worm proteins that belong to the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 (CAP) superfamily are proposed to play key roles in the infection process and the modulation of immune responses in host animals. However, there is limited information on these proteins for most socioeconomically important worms. Here, we review the CAP protein superfamily of Haemonchus contortus (barber's pole worm), a highly significant parasitic roundworm (order Strongylida) of small ruminants. To do this, we mined genome and transcriptomic datasets, predicted and curated full-length amino acid sequences (n = 45), undertook systematic phylogenetic analyses of these data and investigated transcription throughout the life cycle of H. contortus. We inferred functions for selected C. elegans orthologs (including vap-1, vap-2, scl-5 and lon-1) based on genetic networking and by integrating data and published information, and were able to infer that a subset of orthologs and their interaction partners play pivotal roles in growth and development via the insulin-like and/or the TGF-beta signaling pathways. The identification of the important and conserved growth regulator LON-1 led us to appraise the threedimensional structure of this CAP protein by comparative modelling. This model revealed the presence of different topological moieties on the canonical fold of the CAP domain, which coincide with an overall charge separation as indicated by the electrostatic surface potential map. These observations suggest the existence of separate sites for effector binding and receptor interactions, and thus support the proposal that these worm molecules act in similar ways as venoms act as ligands for chemokine receptors or G protein-coupled receptor effectors. In conclusion, this review should guide future molecular studies of these molecules, and could support the development of novel interventions against haemonchosis.

Journal of Cheminformatics, 2015

Background: The increased use of small-molecule compound screening by new users from a variety of... more Background: The increased use of small-molecule compound screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyse and exchange information obtained from screening experiments. While software and spreadsheet solutions exist, there is a need for software that can be easily deployed and is convenient to use. Results: The Java application cApp addresses this need and aids in the handling and storage of information on small-molecule compounds. The software is intended for the appraisal of compounds with respect to their physicochemical properties, analysis in relation to adherence to likeness rules as well as recognition of pan-assay interference components and cross-linking with identical entries in the PubChem Compound Database. Results are displayed in a tabular form in a graphical interface, but can also be written in an HTML or PDF format. The output of data in ASCII format allows for further processing of data using other suitable programs. Other features include similarity searches against user-provided compound libraries and the PubChem Compound Database, as well as compound clustering based on a MaxMin algorithm. Conclusions: cApp is a personal database solution for small-molecule compounds which can handle all major chemical formats. Being a standalone software, it has no other dependency than the Java virtual machine and is thus conveniently deployed. It streamlines the analysis of molecules with respect to physico-chemical properties and drug discovery criteria; cApp is distributed under the GNU

Journal of Molecular Liquids, 2014

Weighted histogram analysis method (WHAM) 18 Solvation structure and association of γ-aminobutyri... more Weighted histogram analysis method (WHAM) 18 Solvation structure and association of γ-aminobutyric acid (GABA) zwitterions in aqueous TFE solutions are in-19 vestigated using molecular dynamics simulation and the AMBER03 force field. Radial distribution functions are 20 used to discuss the effect of solvents on GABA and vice versa. It is shown that GABA causes structure making 21 among water molecules through kosmotropic effect and structure breaking among water and TFE molecules 22 through chaotropic effect. Moreover, the weighted histogram analysis method (WHAM) is used for the calcula-23 tion of potential of mean force (PMF) from MD simulations. Using the extracted PMFs, the association free ener-24 gies and the association equilibrium constants for GABA in TFE and in water are calculated. It is shown that the 25 association of GABA molecules in TFE is more prospective than that in water and the probability of association 26 increases with GABA concentration.

International Studies in the Philosophy of Science, 2013

ABSTRACT In this article, we argue that although Bohr's version of the Copenhagen interpr... more ABSTRACT In this article, we argue that although Bohr's version of the Copenhagen interpretation is in line with several key elements of logical positivism, pragmatism is the closest approximation to a classification of the Copenhagen interpretation, whether or not pragmatists directly influenced the key figures of the interpretation. Pragmatism already encompasses important elements of operationalism and logical positivism, especially the liberalized Carnapian reading of logical positivism. We suggest that some elements of the Copenhagen interpretation, which are in line with logical positivism, are also supported by pragmatism. Some of these elements are empirical realism, fallibilism, holism, and instrumentalism. However, pragmatism goes beyond logical positivism in espousing some other key elements of the Copenhagen interpretation, though imperfectly, such as the correspondence principle, complementarity, and indeterminism.

NeuroQuantology, 2012

In this paper it is claimed that Bohm's holistic, realistic, causally deterministic, non-local th... more In this paper it is claimed that Bohm's holistic, realistic, causally deterministic, non-local theory of the relationship of mind and matter which is based on the key notion of "active information" suffers from an ill inductive reasoning. It is shown that the notion is a special case of the notion of pragmatic information as posed by Roederer which applies merely to natural living systems and artifacts (unnatural nonliving systems). So, the extension of the thesis of active information to the natural nonliving world would count as a violation of the key constituent concepts of pragmatic information and as an ill generalization of Bohm's thesis itself. Active information as 'mind' will be found in biological systems and in some artifacts which represent the biological mind. There is no reason to think of inanimate nature being driven by information. This, in turn, would lead to the substitution of empirical realism for realism, modifying Bohm's ideas to come even closer to the Copenhagen interpretation of quantum mechanics.

Wilson and Walker's Principles and Techniques of Biochemistry and Molecular Biology

International Journal of Hydrogen Energy

International Journal of Hydrogen Energy

Scientific Reports, 2015

All multicellular organisms studied to date have three right open reading frame kinase genes (des... more All multicellular organisms studied to date have three right open reading frame kinase genes (designated riok-1, riok-2 and riok-3). Current evidence indicates that riok-1 and riok-2 have essential roles in ribosome biosynthesis, and that the riok-3 gene assists this process. In the present study, we conducted a detailed bioinformatic analysis of the riok gene family in 25 parasitic flatworms (platyhelminths) for which extensive genomic and transcriptomic data sets are available. We found that none of the flatworms studied have a riok-3 gene, which is unprecedented for multicellular organisms. We propose that, unlike in other eukaryotes, the loss of RIOK-3 from flatworms does not result in an evolutionary disadvantage due to the unique biology and physiology of this phylum. We show that the loss of RIOK-3 coincides with a loss of particular proteins associated with essential cellular pathways linked to cell growth and apoptosis. These findings indicate multiple, key regulatory functions of RIOK-3 in other metazoan species. Taking advantage of a known partial crystal structure of human RIOK-1, molecular modelling revealed variability in nucleotide binding sites between flatworm and human RIOK proteins.

FEBS Journal, 2015

The mycobacterial enzyme Rv1284 is a member of the β-carbonic anhydrase family that has been deem... more The mycobacterial enzyme Rv1284 is a member of the β-carbonic anhydrase family that has been deemed essential for survival of the pathogen. The active site cavity of this dimeric protein is characterised by an exceptionally small volume and harbours a catalytic zinc ion coordinated by two cysteine and one histidine residue side chains. Using the natural products polycarpine and emodin as chemical probes in crystallographic experiments and stopped-flow enzyme assays, we describe here that the catalytic activity can be reversibly inhibited by oxidation. Oxidative conditions lead to removal of one of the active site cysteine residues from the coordination sphere of the catalytic metal ion by engagement in a disulphide bond with another cysteine residue close by. The subsequent loss of the metal ion, which is supported by crystallographic analysis, may thus render the protein catalytically inactive. The oxidative inhibition of Rv1284 can be reversed by exposing the protein to reducing conditions. Since the physical size of the chemical probes used in this study substantially exceeds the active site volume, we hypothesised that these compounds exert their effects from a surface-bound location and identified tyrosine 120 as a critical residue for oxidative inactivation. These findings link conditions of oxidative stress to pH homeostasis of the pathogen. Since oxidative stress and acidification are defence mechanisms employed by the innate immune system of the host, we suggest that Rv1284 may be a component of the mycobacterial survival strategy. This article is protected by copyright. All rights reserved.

Australian Journal of Chemistry, 2014

Journal of Cheminformatics, 2015

Background: The increased use of small-molecule compound screening by new users from a variety of... more Background: The increased use of small-molecule compound screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyse and exchange information obtained from screening experiments. While software and spreadsheet solutions exist, there is a need for software that can be easily deployed and is convenient to use.

Journal of Molecular Liquids

ACS Chemical Neuroscience, 2021

Chemoinformatics appraisal and molecular docking were employed to investigate 225 complexes of 75... more Chemoinformatics appraisal and molecular docking were employed to investigate 225 complexes of 75 schizophrenia antipsychotics with the dopamine receptor subtypes D2R, D3R, and D4R. Considering the effective noncovalent interactions in the subtype-D2 receptor selectivity of antipsychotics, this study evaluated the possible physicochemical properties of ligands underlying the design of safer and more effective antipsychotics. The pan-assay interference compounds (PAINs) include about 25% of typical antipsychotics and 5% of atypicals. Popular antipsychotics like haloperidol, clozapine, risperidone, and aripiprazole are not PAINs. They have stronger interactions with D2R and D4R, but their interactions with D3R are slightly weaker, which is similar to the behavior of dopamine. In contrast to typical antipsychotics, atypical antipsychotics exhibit more noncovalent interactions with D4R than with D2R. These results suggest that selectivity to D2R and D4R comes from the synergy between hydrophobic and hydrogen-bonding interactions through their concomitant occurrence in the form of a hydrogen-bonding site adorned with hydrophobic contacts in antipsychotic-receptor complexes. All the antipsychotics had more synergic interactions with D2R and D4R in comparison with D3R. The atypical antipsychotics made a good distinction between the subtype D2 receptors with high selectivity to D4R. Among the popular antipsychotics, haloperidol, clozapine, and risperidone have hydrophobic-hydrogen-bonding synergy with D4R, while aripiprazole profits with D2R. The most important residue participating in the synergic interactions was threonine for D2R and cysteine for D4R. This work could be useful in informing and guiding future drug discovery and development studies aimed at receptor-specific antipsychotics.

Additional file 1: The software manual accompanies this paper as supplementary information.

Physical Chemistry Research, 2019

AChE is an enzyme that is predominate in a healthy brain, while BChE is considered to play a mino... more AChE is an enzyme that is predominate in a healthy brain, while BChE is considered to play a minor role in regulating the levels of ACh (memory molecule) in the brain. In addition to setting the ACh level, these two enzymes also facilitate Aβ aggregation by forming stable complexes and participate in the abnormal phosphorylation of the tau protein, which also contribute to the development of Alzheimer’s disease (AD). Trace elements including Zn2+, Cu2+, and Fe2+ are found in the brain plaques of Alzheimer’s patients. This study employed tacrine as an efficient inhibitor of cholinesterase and quercetin as a natural metal chelating agent to design a new multi-target-directed ligand, which has been named Tac-Quer. The chelating properties of this ligand have been studied by quantum calculations. The Tac-Quer/Metal binding energies for Zn2+, Cu2+, and Fe2+ are -939. 08, -917.62, and - 694.103 kcal.mol-1, respectively. The cholinesterase enzyme inhibitory activity of the Tac-Quer ligand ...

Applied Surface Science, 2020

The gas-adsorption behaviors of O 2 and H 2 on penta-graphene (PG) and Pt single atom@penta-graph... more The gas-adsorption behaviors of O 2 and H 2 on penta-graphene (PG) and Pt single atom@penta-graphene (Pt-PG) were investigated using density functional theory calculations. To illustrate the importance of the van der Waals (vdW) interactions, in addition to popular local density approximation (LDA) and semilocal Perdew-Burke-Ernzerhof generalized gradient approximation (GGA-PBEsol) functionals, two non-local (vdW-DF2 and rev-vdW-DF2) functionals were investigated through the correlation between energetic, structural, and electronic properties. On the surface of the PG (band gap 2.3 eV), O 2 was strongly physisorbed, which reduced the O 2 /PG band gap to~0.75 eV and created a p-type semiconductor. The H 2 was very weakly physisorbed without any changes in the band gap. On the semimetal Pt-PG (zero band gap), the H 2 and O 2 were strongly chemisorbed which was dissociative for H 2. H 2 adsorption opens a band gap of 1.45 eV, making the H 2 /Pt-PG system a semiconductor. But the O 2 /Pt-PG system remains semimetal. The PG can be used for the detection of O 2 but not for H 2. The presence of the Pt atoms allows the Pt-PG system to detect the H 2 very well. LDA is suggested for investigating H 2 adsorption on both the PG and Pt-PG systems, but the non-local vdWs must be used for the O 2 adsorption study.

Biotechnology Advances, 2015

Parasitic worm proteins that belong to the cysteine-rich secretory proteins, antigen 5 and pathog... more Parasitic worm proteins that belong to the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 (CAP) superfamily are proposed to play key roles in the infection process and the modulation of immune responses in host animals. However, there is limited information on these proteins for most socioeconomically important worms. Here, we review the CAP protein superfamily of Haemonchus contortus (barber's pole worm), a highly significant parasitic roundworm (order Strongylida) of small ruminants. To do this, we mined genome and transcriptomic datasets, predicted and curated full-length amino acid sequences (n = 45), undertook systematic phylogenetic analyses of these data and investigated transcription throughout the life cycle of H. contortus. We inferred functions for selected C. elegans orthologs (including vap-1, vap-2, scl-5 and lon-1) based on genetic networking and by integrating data and published information, and were able to infer that a subset of orthologs and their interaction partners play pivotal roles in growth and development via the insulin-like and/or the TGF-beta signaling pathways. The identification of the important and conserved growth regulator LON-1 led us to appraise the threedimensional structure of this CAP protein by comparative modelling. This model revealed the presence of different topological moieties on the canonical fold of the CAP domain, which coincide with an overall charge separation as indicated by the electrostatic surface potential map. These observations suggest the existence of separate sites for effector binding and receptor interactions, and thus support the proposal that these worm molecules act in similar ways as venoms act as ligands for chemokine receptors or G protein-coupled receptor effectors. In conclusion, this review should guide future molecular studies of these molecules, and could support the development of novel interventions against haemonchosis.

Journal of Cheminformatics, 2015

Background: The increased use of small-molecule compound screening by new users from a variety of... more Background: The increased use of small-molecule compound screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyse and exchange information obtained from screening experiments. While software and spreadsheet solutions exist, there is a need for software that can be easily deployed and is convenient to use. Results: The Java application cApp addresses this need and aids in the handling and storage of information on small-molecule compounds. The software is intended for the appraisal of compounds with respect to their physicochemical properties, analysis in relation to adherence to likeness rules as well as recognition of pan-assay interference components and cross-linking with identical entries in the PubChem Compound Database. Results are displayed in a tabular form in a graphical interface, but can also be written in an HTML or PDF format. The output of data in ASCII format allows for further processing of data using other suitable programs. Other features include similarity searches against user-provided compound libraries and the PubChem Compound Database, as well as compound clustering based on a MaxMin algorithm. Conclusions: cApp is a personal database solution for small-molecule compounds which can handle all major chemical formats. Being a standalone software, it has no other dependency than the Java virtual machine and is thus conveniently deployed. It streamlines the analysis of molecules with respect to physico-chemical properties and drug discovery criteria; cApp is distributed under the GNU

Journal of Molecular Liquids, 2014

Weighted histogram analysis method (WHAM) 18 Solvation structure and association of γ-aminobutyri... more Weighted histogram analysis method (WHAM) 18 Solvation structure and association of γ-aminobutyric acid (GABA) zwitterions in aqueous TFE solutions are in-19 vestigated using molecular dynamics simulation and the AMBER03 force field. Radial distribution functions are 20 used to discuss the effect of solvents on GABA and vice versa. It is shown that GABA causes structure making 21 among water molecules through kosmotropic effect and structure breaking among water and TFE molecules 22 through chaotropic effect. Moreover, the weighted histogram analysis method (WHAM) is used for the calcula-23 tion of potential of mean force (PMF) from MD simulations. Using the extracted PMFs, the association free ener-24 gies and the association equilibrium constants for GABA in TFE and in water are calculated. It is shown that the 25 association of GABA molecules in TFE is more prospective than that in water and the probability of association 26 increases with GABA concentration.

International Studies in the Philosophy of Science, 2013

ABSTRACT In this article, we argue that although Bohr's version of the Copenhagen interpr... more ABSTRACT In this article, we argue that although Bohr's version of the Copenhagen interpretation is in line with several key elements of logical positivism, pragmatism is the closest approximation to a classification of the Copenhagen interpretation, whether or not pragmatists directly influenced the key figures of the interpretation. Pragmatism already encompasses important elements of operationalism and logical positivism, especially the liberalized Carnapian reading of logical positivism. We suggest that some elements of the Copenhagen interpretation, which are in line with logical positivism, are also supported by pragmatism. Some of these elements are empirical realism, fallibilism, holism, and instrumentalism. However, pragmatism goes beyond logical positivism in espousing some other key elements of the Copenhagen interpretation, though imperfectly, such as the correspondence principle, complementarity, and indeterminism.

NeuroQuantology, 2012

In this paper it is claimed that Bohm's holistic, realistic, causally deterministic, non-local th... more In this paper it is claimed that Bohm's holistic, realistic, causally deterministic, non-local theory of the relationship of mind and matter which is based on the key notion of "active information" suffers from an ill inductive reasoning. It is shown that the notion is a special case of the notion of pragmatic information as posed by Roederer which applies merely to natural living systems and artifacts (unnatural nonliving systems). So, the extension of the thesis of active information to the natural nonliving world would count as a violation of the key constituent concepts of pragmatic information and as an ill generalization of Bohm's thesis itself. Active information as 'mind' will be found in biological systems and in some artifacts which represent the biological mind. There is no reason to think of inanimate nature being driven by information. This, in turn, would lead to the substitution of empirical realism for realism, modifying Bohm's ideas to come even closer to the Copenhagen interpretation of quantum mechanics.

Wilson and Walker's Principles and Techniques of Biochemistry and Molecular Biology

International Journal of Hydrogen Energy

International Journal of Hydrogen Energy

Scientific Reports, 2015

All multicellular organisms studied to date have three right open reading frame kinase genes (des... more All multicellular organisms studied to date have three right open reading frame kinase genes (designated riok-1, riok-2 and riok-3). Current evidence indicates that riok-1 and riok-2 have essential roles in ribosome biosynthesis, and that the riok-3 gene assists this process. In the present study, we conducted a detailed bioinformatic analysis of the riok gene family in 25 parasitic flatworms (platyhelminths) for which extensive genomic and transcriptomic data sets are available. We found that none of the flatworms studied have a riok-3 gene, which is unprecedented for multicellular organisms. We propose that, unlike in other eukaryotes, the loss of RIOK-3 from flatworms does not result in an evolutionary disadvantage due to the unique biology and physiology of this phylum. We show that the loss of RIOK-3 coincides with a loss of particular proteins associated with essential cellular pathways linked to cell growth and apoptosis. These findings indicate multiple, key regulatory functions of RIOK-3 in other metazoan species. Taking advantage of a known partial crystal structure of human RIOK-1, molecular modelling revealed variability in nucleotide binding sites between flatworm and human RIOK proteins.

FEBS Journal, 2015

The mycobacterial enzyme Rv1284 is a member of the β-carbonic anhydrase family that has been deem... more The mycobacterial enzyme Rv1284 is a member of the β-carbonic anhydrase family that has been deemed essential for survival of the pathogen. The active site cavity of this dimeric protein is characterised by an exceptionally small volume and harbours a catalytic zinc ion coordinated by two cysteine and one histidine residue side chains. Using the natural products polycarpine and emodin as chemical probes in crystallographic experiments and stopped-flow enzyme assays, we describe here that the catalytic activity can be reversibly inhibited by oxidation. Oxidative conditions lead to removal of one of the active site cysteine residues from the coordination sphere of the catalytic metal ion by engagement in a disulphide bond with another cysteine residue close by. The subsequent loss of the metal ion, which is supported by crystallographic analysis, may thus render the protein catalytically inactive. The oxidative inhibition of Rv1284 can be reversed by exposing the protein to reducing conditions. Since the physical size of the chemical probes used in this study substantially exceeds the active site volume, we hypothesised that these compounds exert their effects from a surface-bound location and identified tyrosine 120 as a critical residue for oxidative inactivation. These findings link conditions of oxidative stress to pH homeostasis of the pathogen. Since oxidative stress and acidification are defence mechanisms employed by the innate immune system of the host, we suggest that Rv1284 may be a component of the mycobacterial survival strategy. This article is protected by copyright. All rights reserved.

Australian Journal of Chemistry, 2014

Journal of Cheminformatics, 2015

Background: The increased use of small-molecule compound screening by new users from a variety of... more Background: The increased use of small-molecule compound screening by new users from a variety of different academic backgrounds calls for adequate software to administer, appraise, analyse and exchange information obtained from screening experiments. While software and spreadsheet solutions exist, there is a need for software that can be easily deployed and is convenient to use.