A cell-based high-throughput screen to identify small molecular weight stimulators of the innate ... more A cell-based high-throughput screen to identify small molecular weight stimulators of the innate immune system revealed substituted pyrimido[5,4-b]indoles as potent NFκB activators. The most potent hit compound selectively stimulated Toll-like receptor 4 (TLR4) in human and mouse cells. Synthetic modifications of the pyrimido[5,4-b]indole scaffold at the carboxamide, N-3, and N-5 positions revealed differential TLR4 dependent production of NFκB and type I interferon associated cytokines, IL-6 and interferon γ-induced protein 10 (IP-10) respectively. Specifically, a subset of compounds bearing phenyl and substituted phenyl carboxamides induced lower IL-6 release while maintaining higher IP-10 production, skewing toward the type I interferon pathway. Substitution at N-5 with short alkyl substituents reduced the cytotoxicity of the leading hit compound. Computational studies supported that active compounds appeared to bind primarily to MD-2 in the TLR4/MD-2 complex. These small molecules, which stimulate innate immune cells with minimal toxicity, could potentially be used as adjuvants or immune modulators.
Proceedings of the National Academy of Sciences, 2020
Significance Transcription factors in the bHLH family are potentially relevant for tumor growth. ... more Significance Transcription factors in the bHLH family are potentially relevant for tumor growth. Activation requires homodimerization or heterodimerization. Thus, the dimerization step is a likely significant drug target. The oligodendrocyte transcription factor 2 (OLIG2) is overexpressed in gliomas. Here, we developed a fluorescence cross-correlation spectroscopy protocol to examine 10 compounds selected using a pharmacophore-based computational strategy targeting OLIG2 dimerization. We showed that the potency to interact with OLIG2 dimerization in live cells correlates with carcinostatic efficacy. The data indicate a promising approach toward drug development targeting transcription factor overactivity and protein–protein interaction more generally.
Context: SARS CoV 2 induced cytokine storm is the major cause of COVID 19 related deaths. Patient... more Context: SARS CoV 2 induced cytokine storm is the major cause of COVID 19 related deaths. Patients have been treated with drugs that work by inhibiting a specific protein partly responsible for the cytokines production. This approach provided very limited success, since there are multiple proteins involved in the complex cell signaling disease mechanisms. Objective: To elucidate using machine learning (ML) the set of drugs targeting a group of proteins involved in the mechanism of cytokine storm. Methods: We selected for targeting five proteins: Angiotensin II receptor type 1 (AT1R), A disintegrin and metalloprotease 17 (ADAM17), Nuclear Factor Kappa B (NF 𝜅B), Janus kinase 1 (JAK1) and Signal Transducer and Activator of Transcription 3 (STAT3) that are involved in the SARS CoV 2 induced cytokine storm pathway. We developed ML models for these five proteins, using known active inhibitors. After developing the model for each of these proteins, FDA-approved drugs were screened to find...
Context: SARS CoV 2 induced cytokine storm is the major cause of COVID 19 related deaths. Patient... more Context: SARS CoV 2 induced cytokine storm is the major cause of COVID 19 related deaths. Patients have been treated with drugs that work by inhibiting a specific protein partly responsible for the cytokines production. This approach provided very limited success, since there are multiple proteins involved in the complex cell signaling disease mechanisms. Objective: To elucidate using machine learning (ML) the set of drugs targeting a group of proteins involved in the mechanism of cytokine storm. Methods: We selected for targeting five proteins: Angiotensin II receptor type 1 (AT1R), A disintegrin and metalloprotease 17 (ADAM17), Nuclear Factor Kappa B (NF 𝜅B), Janus kinase 1 (JAK1) and Signal Transducer and Activator of Transcription 3 (STAT3) that are involved in the SARS CoV 2 induced cytokine storm pathway. We developed ML models for these five proteins, using known active inhibitors. After developing the model for each of these proteins, FDA-approved drugs were screened to find...
Background: In the current COVID-19 pandemic, with an absence of approved drugs and widely access... more Background: In the current COVID-19 pandemic, with an absence of approved drugs and widely accessible vaccines, repurposing existing drugs is vital to quickly developing a treatment for the disease. Methods: In this study, we used a dataset consisting of sequences of viral proteins and chemical structures of pharmaceutical drugs for known drug-target interactions (DTIs) and artificially generated non-interacting DTIs to train a binary classifier with the ability to predict new DTIs. Random Forest (RF), deep neural network (DNN), and convolutional neural networks (CNN) were tested. The CNN and RF models were selected for the classification task. Results: The models generalized well to the given DTI data and were used to predict DTIs involving SARS-CoV-2 nonstructural proteins (NSPs). We elucidated (with the CNN) 29 drugs involved in 82 DTIs with a 97% probability of interaction, 44 DTIs of which had a 99% probability of interaction, to treat COVID-19. The RF elucidated 6 drugs involved in 17 DTIs with a 90% probability of interacting. Conclusions: These results give new insight into possible inhibitors of the viral proteins beyond pharmacophore models and molecular docking procedures used in recent studies.
P38-alpha (MAPK14) is a protein kinase that is implicated in the pathological mechanisms of BAG3 ... more P38-alpha (MAPK14) is a protein kinase that is implicated in the pathological mechanisms of BAG3 P209L myofibrillar myopathy, cancers, Alzheimer’s disease and other diseases like rheumatoid arthritis. Inhibition of p38 has shown promise as treatment for these diseases. Traditional drug discovery methods were unable to create both effective and safe small molecule inhibitors, so we used machine learning to elucidate potential p38 blockers from existing FDA-approved drugs. Using available bioactivity data, we determined the best existing p38 inhibitors and applied fingerprint clustering to isolate the compounds with similar structures. Descriptors were calculated for these clustered compounds and the most important of these descriptors were determined through a machine-learning based feature selection algorithm. This data served as the training set for a deep neural network that was fine-tuned to a 92% validation accuracy. The neural network model was applied to a database of FDA-appr...
Development of non-invasive diagnostic tests which can immediately yield guidance in clinics, red... more Development of non-invasive diagnostic tests which can immediately yield guidance in clinics, reducing the number of samples sent for laboratory testing, has the potential to revolutionize medical diagnostics improving patient outcomes, doctor’s workloads, and healthcare costs. It is difficult to imagine a testing method less invasive than measurement of salivary metabolites by swab or spit. Coupling data from this incredibly convenient measurement to an automated decision-making engine can provide clinicians with immediate feedback on the status of their patients. The aim of this research is to lay the foundation for a system, which when employed in dental practices can help to stratify between patients with periodontitis and oral cancers and illuminate metabolic networks important to both diseases. We built machine learning models trained on QSAR descriptors of metabolites whose concentrations changed drastically between the two diseases and used these same metabolites to illumina...
Purpose: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deat... more Purpose: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths worldwide, pushing the urgent need for an efficient treatment. Nonstructural protein 15 (NSP15) is a promising target due to its importance for SARS-CoV-2’s evasion of the host’s innate immune response. Methods: Using the crystal structure of SARS-CoV-2 NSP15 endoribonuclease, we developed a pharmacophore model of the functional centers in the NSP15 inhibitor’s binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. The conformations of these compounds underwent 3D fingerprint similarity clustering, and possible conformers were docked to the NSP15 binding pocket. We also simulated docking of random compounds to the NSP15 binding pocket for comparison. Results: This search identified 170 compounds as potential inhibitors of SARS-CoV-2 NSP15. The mean free energy of docking for the group of potential inhibitors were significantly l...
Bovine leukemia virus (BLV) is a virus that infects cattle around the world and is very similar t... more Bovine leukemia virus (BLV) is a virus that infects cattle around the world and is very similar to the human T-cell leukemia virus (HTLV), which causes adult T-cell leukemia/lymphoma (ATL). Recently, presence of BLV DNA and protein was demonstrated in commercial bovine products and in humans. BLV DNA is generally found at higher rates in humans who have or will develop breast cancer, according to research done with subjects from several countries. These findings have led to a hypothesis that BLV transmission plays a role in breast cancer oncogenesis in humans. Here we summarize the current knowledge in the field.
Feline cancers have not been studied as extensively as canine cancers, though they may offer simi... more Feline cancers have not been studied as extensively as canine cancers, though they may offer similar advantages, with cats being immunocompetent animals subject to similar conditions as their human counterparts. The most common feline cancers include lymphoma, squamous cell carcinoma, sarcoma, and mammary tumors, though mast cell tumors were also investigated in this review. As the pathogenesis of many feline cancers remains unclear, this study seeks to elucidate some molecular mechanisms behind feline cancers. Feline lymphoma has been commonly associated with feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV), though in recent years it has appeared more as lymphoma of the gastrointestinal tract. Chromosomal alterations (translocations) due to the virus-associated lymphoma, as well as aberrant gene expression (such as in COX-2 and MDR1) have been identified in the past. While feline lymphoma may be divided into many subtypes, feline sarcoma may be divided into two ...
Type 2 diabetes is a chronic condition encompassing many metabolic processes throughout the body.... more Type 2 diabetes is a chronic condition encompassing many metabolic processes throughout the body. Glucose and lipid transporters are involved in many of these critical metabolic processes and pathways, and are linked to the development and symptoms of type 2 diabetes. Therapeutic opportunities utilizing these transporters have already begun with the gliflozin drug class of inhibitors of sodium glucose linked co-transporters (SGLT). A range of transporter families: SLC5A (SGLT), SLC2A (GLUT), and ATP binding cassette (ABC) transporters are either connected to glucose or cholesterol homeostasis, significant in a systemic disease like diabetes type 2. Elucidating the roles of these transporters in type 2 diabetes is vital in establishing new and effective options for treatment.
Journal of Bioinformatics and Computational Biology, 2008
Many major facilitator superfamily (MFS) transporters have similar 12-transmembrane α-helical top... more Many major facilitator superfamily (MFS) transporters have similar 12-transmembrane α-helical topologies with two six-helix halves connected by a long loop. In humans, these transporters participate in key physiological processes and are also, as in the case of members of the organic anion transporter (OAT) family, of pharmaceutical interest. Recently, crystal structures of two bacterial representatives of the MFS family — the glycerol-3-phosphate transporter (GlpT) and lac-permease (LacY) — have been solved and, because of assumptions regarding the high structural conservation of this family, there is hope that the results can be applied to mammalian transporters as well. Based on crystallography, it has been suggested that a major conformational "switching" mechanism accounts for ligand transport by MFS proteins. This conformational switch would then allow periodic changes in the overall transporter configuration, resulting in its cyclic opening to the periplasm or cytop...
Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers... more Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers, and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom molecular dynamics, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteris...
We have studied the thermal inactivation at 37°C of wild type and mutant ChE2 (C310A, F312I, C466... more We have studied the thermal inactivation at 37°C of wild type and mutant ChE2 (C310A, F312I, C466A, C310A/F312I, and C310A/C466A) from amphioxus (Branchiostoma floridae) expressed in vitro in COS-7 monkey cells under three sets of conditions: 30°C for 48 h, 30°for 24 h and C37°C for 24 h, and 37°C for 48 h. We found biphasic denaturation curves for all enzymes and conditions, except wild type and C310A ChE2 expressed at 30°C for 48 h. Generally, single mutants are more unstable than wild type, and the double mutants are even more unstable. We propose a model involving stable and unstable conformations of the enzymes to explain these results, and we discuss the implications of the model. We also found a correlation between the melting temperature of the ChEs and the rates at which they denature at 37°C, with the denaturation of the unstable conformation dominating the relationship. Reversible cholinergic inhibitors protect the ChEs from thermal denaturation, and in some cases produce monophasic denaturation curves; we also propose a model to explain this stabilization.
Organic anion transporter 1 (Oat1), first identified as NKT, is a multispecific transporter respo... more Organic anion transporter 1 (Oat1), first identified as NKT, is a multispecific transporter responsible for the handling of drugs and toxins in the kidney and choroid plexus, but its normal physiological role appears to be in small molecule metabolite regulation. Metabolites transported by Oat1 and which are altered in the blood and urine of the murine Oat1 knockout, may serve as templates for further drug design. This may lead to better tissue targeting of drugs or design of Oat1 inhibitors that prolong the half-life of current drugs. Due to the multispecificity of the transporter, 19 of known targeted metabolites have different chemical structures and properties that make constructing a common pharmacophore model difficult. Here we propose an approach that clustered the metabolites into four distinct groups which allowed for the construction of a consensus pharmacophore for each cluster. The screening of commercial molecular databases determined the top candidates whose interaction with Oat1 was confirmed in an experimental model of organic anion transport. Thus, these candidate selections represent potential molecules for further drug design.
A cell-based high-throughput screen to identify small molecular weight stimulators of the innate ... more A cell-based high-throughput screen to identify small molecular weight stimulators of the innate immune system revealed substituted pyrimido[5,4-b]indoles as potent NFκB activators. The most potent hit compound selectively stimulated Toll-like receptor 4 (TLR4) in human and mouse cells. Synthetic modifications of the pyrimido[5,4-b]indole scaffold at the carboxamide, N-3, and N-5 positions revealed differential TLR4 dependent production of NFκB and type I interferon associated cytokines, IL-6 and interferon γ-induced protein 10 (IP-10) respectively. Specifically, a subset of compounds bearing phenyl and substituted phenyl carboxamides induced lower IL-6 release while maintaining higher IP-10 production, skewing toward the type I interferon pathway. Substitution at N-5 with short alkyl substituents reduced the cytotoxicity of the leading hit compound. Computational studies supported that active compounds appeared to bind primarily to MD-2 in the TLR4/MD-2 complex. These small molecules, which stimulate innate immune cells with minimal toxicity, could potentially be used as adjuvants or immune modulators.
Proceedings of the National Academy of Sciences, 2020
Significance Transcription factors in the bHLH family are potentially relevant for tumor growth. ... more Significance Transcription factors in the bHLH family are potentially relevant for tumor growth. Activation requires homodimerization or heterodimerization. Thus, the dimerization step is a likely significant drug target. The oligodendrocyte transcription factor 2 (OLIG2) is overexpressed in gliomas. Here, we developed a fluorescence cross-correlation spectroscopy protocol to examine 10 compounds selected using a pharmacophore-based computational strategy targeting OLIG2 dimerization. We showed that the potency to interact with OLIG2 dimerization in live cells correlates with carcinostatic efficacy. The data indicate a promising approach toward drug development targeting transcription factor overactivity and protein–protein interaction more generally.
Context: SARS CoV 2 induced cytokine storm is the major cause of COVID 19 related deaths. Patient... more Context: SARS CoV 2 induced cytokine storm is the major cause of COVID 19 related deaths. Patients have been treated with drugs that work by inhibiting a specific protein partly responsible for the cytokines production. This approach provided very limited success, since there are multiple proteins involved in the complex cell signaling disease mechanisms. Objective: To elucidate using machine learning (ML) the set of drugs targeting a group of proteins involved in the mechanism of cytokine storm. Methods: We selected for targeting five proteins: Angiotensin II receptor type 1 (AT1R), A disintegrin and metalloprotease 17 (ADAM17), Nuclear Factor Kappa B (NF 𝜅B), Janus kinase 1 (JAK1) and Signal Transducer and Activator of Transcription 3 (STAT3) that are involved in the SARS CoV 2 induced cytokine storm pathway. We developed ML models for these five proteins, using known active inhibitors. After developing the model for each of these proteins, FDA-approved drugs were screened to find...
Context: SARS CoV 2 induced cytokine storm is the major cause of COVID 19 related deaths. Patient... more Context: SARS CoV 2 induced cytokine storm is the major cause of COVID 19 related deaths. Patients have been treated with drugs that work by inhibiting a specific protein partly responsible for the cytokines production. This approach provided very limited success, since there are multiple proteins involved in the complex cell signaling disease mechanisms. Objective: To elucidate using machine learning (ML) the set of drugs targeting a group of proteins involved in the mechanism of cytokine storm. Methods: We selected for targeting five proteins: Angiotensin II receptor type 1 (AT1R), A disintegrin and metalloprotease 17 (ADAM17), Nuclear Factor Kappa B (NF 𝜅B), Janus kinase 1 (JAK1) and Signal Transducer and Activator of Transcription 3 (STAT3) that are involved in the SARS CoV 2 induced cytokine storm pathway. We developed ML models for these five proteins, using known active inhibitors. After developing the model for each of these proteins, FDA-approved drugs were screened to find...
Background: In the current COVID-19 pandemic, with an absence of approved drugs and widely access... more Background: In the current COVID-19 pandemic, with an absence of approved drugs and widely accessible vaccines, repurposing existing drugs is vital to quickly developing a treatment for the disease. Methods: In this study, we used a dataset consisting of sequences of viral proteins and chemical structures of pharmaceutical drugs for known drug-target interactions (DTIs) and artificially generated non-interacting DTIs to train a binary classifier with the ability to predict new DTIs. Random Forest (RF), deep neural network (DNN), and convolutional neural networks (CNN) were tested. The CNN and RF models were selected for the classification task. Results: The models generalized well to the given DTI data and were used to predict DTIs involving SARS-CoV-2 nonstructural proteins (NSPs). We elucidated (with the CNN) 29 drugs involved in 82 DTIs with a 97% probability of interaction, 44 DTIs of which had a 99% probability of interaction, to treat COVID-19. The RF elucidated 6 drugs involved in 17 DTIs with a 90% probability of interacting. Conclusions: These results give new insight into possible inhibitors of the viral proteins beyond pharmacophore models and molecular docking procedures used in recent studies.
P38-alpha (MAPK14) is a protein kinase that is implicated in the pathological mechanisms of BAG3 ... more P38-alpha (MAPK14) is a protein kinase that is implicated in the pathological mechanisms of BAG3 P209L myofibrillar myopathy, cancers, Alzheimer’s disease and other diseases like rheumatoid arthritis. Inhibition of p38 has shown promise as treatment for these diseases. Traditional drug discovery methods were unable to create both effective and safe small molecule inhibitors, so we used machine learning to elucidate potential p38 blockers from existing FDA-approved drugs. Using available bioactivity data, we determined the best existing p38 inhibitors and applied fingerprint clustering to isolate the compounds with similar structures. Descriptors were calculated for these clustered compounds and the most important of these descriptors were determined through a machine-learning based feature selection algorithm. This data served as the training set for a deep neural network that was fine-tuned to a 92% validation accuracy. The neural network model was applied to a database of FDA-appr...
Development of non-invasive diagnostic tests which can immediately yield guidance in clinics, red... more Development of non-invasive diagnostic tests which can immediately yield guidance in clinics, reducing the number of samples sent for laboratory testing, has the potential to revolutionize medical diagnostics improving patient outcomes, doctor’s workloads, and healthcare costs. It is difficult to imagine a testing method less invasive than measurement of salivary metabolites by swab or spit. Coupling data from this incredibly convenient measurement to an automated decision-making engine can provide clinicians with immediate feedback on the status of their patients. The aim of this research is to lay the foundation for a system, which when employed in dental practices can help to stratify between patients with periodontitis and oral cancers and illuminate metabolic networks important to both diseases. We built machine learning models trained on QSAR descriptors of metabolites whose concentrations changed drastically between the two diseases and used these same metabolites to illumina...
Purpose: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deat... more Purpose: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths worldwide, pushing the urgent need for an efficient treatment. Nonstructural protein 15 (NSP15) is a promising target due to its importance for SARS-CoV-2’s evasion of the host’s innate immune response. Methods: Using the crystal structure of SARS-CoV-2 NSP15 endoribonuclease, we developed a pharmacophore model of the functional centers in the NSP15 inhibitor’s binding pocket. With this model, we conducted data mining of the conformational database of FDA-approved drugs. The conformations of these compounds underwent 3D fingerprint similarity clustering, and possible conformers were docked to the NSP15 binding pocket. We also simulated docking of random compounds to the NSP15 binding pocket for comparison. Results: This search identified 170 compounds as potential inhibitors of SARS-CoV-2 NSP15. The mean free energy of docking for the group of potential inhibitors were significantly l...
Bovine leukemia virus (BLV) is a virus that infects cattle around the world and is very similar t... more Bovine leukemia virus (BLV) is a virus that infects cattle around the world and is very similar to the human T-cell leukemia virus (HTLV), which causes adult T-cell leukemia/lymphoma (ATL). Recently, presence of BLV DNA and protein was demonstrated in commercial bovine products and in humans. BLV DNA is generally found at higher rates in humans who have or will develop breast cancer, according to research done with subjects from several countries. These findings have led to a hypothesis that BLV transmission plays a role in breast cancer oncogenesis in humans. Here we summarize the current knowledge in the field.
Feline cancers have not been studied as extensively as canine cancers, though they may offer simi... more Feline cancers have not been studied as extensively as canine cancers, though they may offer similar advantages, with cats being immunocompetent animals subject to similar conditions as their human counterparts. The most common feline cancers include lymphoma, squamous cell carcinoma, sarcoma, and mammary tumors, though mast cell tumors were also investigated in this review. As the pathogenesis of many feline cancers remains unclear, this study seeks to elucidate some molecular mechanisms behind feline cancers. Feline lymphoma has been commonly associated with feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV), though in recent years it has appeared more as lymphoma of the gastrointestinal tract. Chromosomal alterations (translocations) due to the virus-associated lymphoma, as well as aberrant gene expression (such as in COX-2 and MDR1) have been identified in the past. While feline lymphoma may be divided into many subtypes, feline sarcoma may be divided into two ...
Type 2 diabetes is a chronic condition encompassing many metabolic processes throughout the body.... more Type 2 diabetes is a chronic condition encompassing many metabolic processes throughout the body. Glucose and lipid transporters are involved in many of these critical metabolic processes and pathways, and are linked to the development and symptoms of type 2 diabetes. Therapeutic opportunities utilizing these transporters have already begun with the gliflozin drug class of inhibitors of sodium glucose linked co-transporters (SGLT). A range of transporter families: SLC5A (SGLT), SLC2A (GLUT), and ATP binding cassette (ABC) transporters are either connected to glucose or cholesterol homeostasis, significant in a systemic disease like diabetes type 2. Elucidating the roles of these transporters in type 2 diabetes is vital in establishing new and effective options for treatment.
Journal of Bioinformatics and Computational Biology, 2008
Many major facilitator superfamily (MFS) transporters have similar 12-transmembrane α-helical top... more Many major facilitator superfamily (MFS) transporters have similar 12-transmembrane α-helical topologies with two six-helix halves connected by a long loop. In humans, these transporters participate in key physiological processes and are also, as in the case of members of the organic anion transporter (OAT) family, of pharmaceutical interest. Recently, crystal structures of two bacterial representatives of the MFS family — the glycerol-3-phosphate transporter (GlpT) and lac-permease (LacY) — have been solved and, because of assumptions regarding the high structural conservation of this family, there is hope that the results can be applied to mammalian transporters as well. Based on crystallography, it has been suggested that a major conformational "switching" mechanism accounts for ligand transport by MFS proteins. This conformational switch would then allow periodic changes in the overall transporter configuration, resulting in its cyclic opening to the periplasm or cytop...
Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers... more Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers, and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom molecular dynamics, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteris...
We have studied the thermal inactivation at 37°C of wild type and mutant ChE2 (C310A, F312I, C466... more We have studied the thermal inactivation at 37°C of wild type and mutant ChE2 (C310A, F312I, C466A, C310A/F312I, and C310A/C466A) from amphioxus (Branchiostoma floridae) expressed in vitro in COS-7 monkey cells under three sets of conditions: 30°C for 48 h, 30°for 24 h and C37°C for 24 h, and 37°C for 48 h. We found biphasic denaturation curves for all enzymes and conditions, except wild type and C310A ChE2 expressed at 30°C for 48 h. Generally, single mutants are more unstable than wild type, and the double mutants are even more unstable. We propose a model involving stable and unstable conformations of the enzymes to explain these results, and we discuss the implications of the model. We also found a correlation between the melting temperature of the ChEs and the rates at which they denature at 37°C, with the denaturation of the unstable conformation dominating the relationship. Reversible cholinergic inhibitors protect the ChEs from thermal denaturation, and in some cases produce monophasic denaturation curves; we also propose a model to explain this stabilization.
Organic anion transporter 1 (Oat1), first identified as NKT, is a multispecific transporter respo... more Organic anion transporter 1 (Oat1), first identified as NKT, is a multispecific transporter responsible for the handling of drugs and toxins in the kidney and choroid plexus, but its normal physiological role appears to be in small molecule metabolite regulation. Metabolites transported by Oat1 and which are altered in the blood and urine of the murine Oat1 knockout, may serve as templates for further drug design. This may lead to better tissue targeting of drugs or design of Oat1 inhibitors that prolong the half-life of current drugs. Due to the multispecificity of the transporter, 19 of known targeted metabolites have different chemical structures and properties that make constructing a common pharmacophore model difficult. Here we propose an approach that clustered the metabolites into four distinct groups which allowed for the construction of a consensus pharmacophore for each cluster. The screening of commercial molecular databases determined the top candidates whose interaction with Oat1 was confirmed in an experimental model of organic anion transport. Thus, these candidate selections represent potential molecules for further drug design.
Uploads
Papers by Igor Tsigelny