Pub Date : 2024-06-18DOI: 10.1021/acs.jcim.4c00775
Ana M Muñoz, Víctor H Orozco, Lina M Hoyos, Luis F Giraldo, Cesar A Pérez
Molecularly imprinted polymers (MIPs) have emerged as bespoke materials with versatile molecular applications. In this study, we propose a proof of concept for a methodology employing molecular dynamics (MD) simulations to guide the selection of functional monomers for curcuminoid binding in MIPs. Curcumin, demethoxycurcumin, and bisdemethoxycurcumin are phenolic compounds widely employed as spices, pigments, additives, and therapeutic agents, representing the three main curcuminoids of interest. Through MD simulations, we investigated prepolymerization mixtures composed of various functional monomers, including acrylamide (ACA), acrylic acid (AA), methacrylic acid (MAA), and N-vinylpyrrolidone (NVP), with ethylene glycol dimethacrylate (EGDMA) as the cross-linker and acetonitrile as the solvent. Curcumin was selected as the template molecule due to its structural similarity to the other curcuminoids. Notably, the prepolymerization mixture containing NVP as the functional monomer demonstrated superior molecular recognition capabilities toward curcumin. This observation was supported by higher functional monomer molecules surrounding the template, a lower total nonbonded energy between the template and monomer, and a greater number of hydrogen bonds in the aggregate. These findings suggest a stronger affinity between the functional monomer NVP and the template. We synthesized, characterized, and conducted binding tests on the MIPs to validate the MD simulation results. The experimental binding tests confirmed that the MIP-NVP exhibited higher binding capacity. Consequently, based on MD simulations, our computational methodology effectively guided the selection of the functional monomer, leading to MIPs with binding capacity for curcuminoids. The outcomes of this study provide a valuable reference for the rational design of MIPs through MD simulations, facilitating the selection of components for MIPs. This computational approach holds the potential for extension to other templates, establishing a robust methodology for the rational design of MIPs.
{"title":"Rational Design of Molecularly Imprinted Polymers for Curcuminoids Binding: Computational and Experimental Approaches for the Selection of Functional Monomers.","authors":"Ana M Muñoz, Víctor H Orozco, Lina M Hoyos, Luis F Giraldo, Cesar A Pérez","doi":"10.1021/acs.jcim.4c00775","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00775","url":null,"abstract":"<p><p>Molecularly imprinted polymers (MIPs) have emerged as bespoke materials with versatile molecular applications. In this study, we propose a proof of concept for a methodology employing molecular dynamics (MD) simulations to guide the selection of functional monomers for curcuminoid binding in MIPs. Curcumin, demethoxycurcumin, and bisdemethoxycurcumin are phenolic compounds widely employed as spices, pigments, additives, and therapeutic agents, representing the three main curcuminoids of interest. Through MD simulations, we investigated prepolymerization mixtures composed of various functional monomers, including acrylamide (ACA), acrylic acid (AA), methacrylic acid (MAA), and <i>N</i>-vinylpyrrolidone (NVP), with ethylene glycol dimethacrylate (EGDMA) as the cross-linker and acetonitrile as the solvent. Curcumin was selected as the template molecule due to its structural similarity to the other curcuminoids. Notably, the prepolymerization mixture containing NVP as the functional monomer demonstrated superior molecular recognition capabilities toward curcumin. This observation was supported by higher functional monomer molecules surrounding the template, a lower total nonbonded energy between the template and monomer, and a greater number of hydrogen bonds in the aggregate. These findings suggest a stronger affinity between the functional monomer NVP and the template. We synthesized, characterized, and conducted binding tests on the MIPs to validate the MD simulation results. The experimental binding tests confirmed that the MIP-NVP exhibited higher binding capacity. Consequently, based on MD simulations, our computational methodology effectively guided the selection of the functional monomer, leading to MIPs with binding capacity for curcuminoids. The outcomes of this study provide a valuable reference for the rational design of MIPs through MD simulations, facilitating the selection of components for MIPs. This computational approach holds the potential for extension to other templates, establishing a robust methodology for the rational design of MIPs.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141416615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18DOI: 10.1021/acs.jcim.4c00591
Pu Jiang, Cong Zhang, Hongshuang Wang, Penghui Li, Xiubo Du, Yibo Wang, Ekaterina Lyukmanova, Cong Lin, Xiaohui Wang
Psychoactive substances, including morphine and methamphetamine, have been shown to interact with the classic innate immune receptor Toll-like receptor 4 (TLR4) and its partner protein myeloid differentiation protein 2 (MD2) in a nonenantioselective manner. (−)-Nicotine, the primary alkaloid in tobacco and a key component of highly addictive cigarettes, targets the TLR4/MD2, influencing TLR4 signaling pathways. Existing as two enantiomers, the stereoselective recognition of nicotine by TLR4/MD2 in the context of the innate immune response remains unclear. In this study, we synthesized (+)-nicotine and investigated its effects alongside (−)-nicotine on lipopolysaccharide (LPS)-induced TLR4 signaling. (−)-Nicotine dose-dependently inhibited proinflammatory factors such as tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), and cyclooxygenase-2 (COX-2). In contrast, (+)-nicotine showed no such inhibitory effects. Molecular dynamics simulations revealed that (−)-nicotine exhibited a stronger affinity with the TLR4 coreceptor MD2 than (+)-nicotine. Additionally, in silico simulations revealed that both nicotine enantiomers initially attach to the entrance of the MD2 cavity, creating a metastable state before they fully enter the cavity. In the metastable state, (−)-nicotine established more stable interactions with the surrounding residues at the entrance of the MD2 cavity compared to those of (+)-nicotine. This highlights the crucial role of the MD2 cavity entrance in the chiral recognition of nicotine. These findings provide valuable insights into the distinct interactions between nicotine enantiomers and the TLR4 coreceptor MD2, underscoring the enantioselective effect of nicotine on modulating TLR4 signaling.
{"title":"Nicotine Enantioselectively Targets Myeloid Differentiation Protein 2 and Inhibits the Toll-like Receptor 4 Signaling","authors":"Pu Jiang, Cong Zhang, Hongshuang Wang, Penghui Li, Xiubo Du, Yibo Wang, Ekaterina Lyukmanova, Cong Lin, Xiaohui Wang","doi":"10.1021/acs.jcim.4c00591","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00591","url":null,"abstract":"Psychoactive substances, including morphine and methamphetamine, have been shown to interact with the classic innate immune receptor Toll-like receptor 4 (TLR4) and its partner protein myeloid differentiation protein 2 (MD2) in a nonenantioselective manner. (−)-Nicotine, the primary alkaloid in tobacco and a key component of highly addictive cigarettes, targets the TLR4/MD2, influencing TLR4 signaling pathways. Existing as two enantiomers, the stereoselective recognition of nicotine by TLR4/MD2 in the context of the innate immune response remains unclear. In this study, we synthesized (+)-nicotine and investigated its effects alongside (−)-nicotine on lipopolysaccharide (LPS)-induced TLR4 signaling. (−)-Nicotine dose-dependently inhibited proinflammatory factors such as tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), and cyclooxygenase-2 (COX-2). In contrast, (+)-nicotine showed no such inhibitory effects. Molecular dynamics simulations revealed that (−)-nicotine exhibited a stronger affinity with the TLR4 coreceptor MD2 than (+)-nicotine. Additionally, in silico simulations revealed that both nicotine enantiomers initially attach to the entrance of the MD2 cavity, creating a metastable state before they fully enter the cavity. In the metastable state, (−)-nicotine established more stable interactions with the surrounding residues at the entrance of the MD2 cavity compared to those of (+)-nicotine. This highlights the crucial role of the MD2 cavity entrance in the chiral recognition of nicotine. These findings provide valuable insights into the distinct interactions between nicotine enantiomers and the TLR4 coreceptor MD2, underscoring the enantioselective effect of nicotine on modulating TLR4 signaling.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18DOI: 10.1021/acs.jcim.3c01195
Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos
Beta-N-methylamino-l-alanine (BMAA) is a potential neurotoxic nonprotein amino acid, which can reach the human body through the food chain. When BMAA interacts with bicarbonate in the human body, carbamate adducts are produced, which share a high structural similarity with the neurotransmitter glutamate. It is believed that BMAA and its l-carbamate adducts bind in the glutamate binding site of ionotropic glutamate receptor 2 (GluR2). Chronic exposure to BMAA and its adducts could cause neurological illness such as neurodegenerative diseases. However, the mechanism of BMAA action and its carbamate adducts bound to GluR2 has not yet been elucidated. Here, we investigate the binding modes and the affinity of BMAA and its carbamate adducts to GluR2 in comparison to the natural agonist, glutamate, to understand whether these can act as GluR2 modulators. Initially, we perform molecular dynamics simulations of BMAA and its carbamate adducts bound to GluR2 to examine the stability of the ligands in the S1/S2 ligand-binding core of the receptor. In addition, we utilize alchemical free energy calculations to compute the difference in the free energy of binding of the beta-carbamate adduct of BMAA to GluR2 compared to that of glutamate. Our findings indicate that carbamate adducts of BMAA and glutamate remain stable in the binding site of the GluR2 compared to BMAA. Additionally, alchemical free energy results reveal that glutamate and the beta-carbamate adduct of BMAA have comparable binding affinity to the GluR2. These results provide a rationale that BMAA carbamate adducts may be, in fact, the modulators of GluR2 and not BMAA itself.
{"title":"Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators","authors":"Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos","doi":"10.1021/acs.jcim.3c01195","DOIUrl":"https://doi.org/10.1021/acs.jcim.3c01195","url":null,"abstract":"Beta-<i>N</i>-methylamino-<span>l</span>-alanine (BMAA) is a potential neurotoxic nonprotein amino acid, which can reach the human body through the food chain. When BMAA interacts with bicarbonate in the human body, carbamate adducts are produced, which share a high structural similarity with the neurotransmitter glutamate. It is believed that BMAA and its <span>l</span>-carbamate adducts bind in the glutamate binding site of ionotropic glutamate receptor 2 (GluR2). Chronic exposure to BMAA and its adducts could cause neurological illness such as neurodegenerative diseases. However, the mechanism of BMAA action and its carbamate adducts bound to GluR2 has not yet been elucidated. Here, we investigate the binding modes and the affinity of BMAA and its carbamate adducts to GluR2 in comparison to the natural agonist, glutamate, to understand whether these can act as GluR2 modulators. Initially, we perform molecular dynamics simulations of BMAA and its carbamate adducts bound to GluR2 to examine the stability of the ligands in the S1/S2 ligand-binding core of the receptor. In addition, we utilize alchemical free energy calculations to compute the difference in the free energy of binding of the beta-carbamate adduct of BMAA to GluR2 compared to that of glutamate. Our findings indicate that carbamate adducts of BMAA and glutamate remain stable in the binding site of the GluR2 compared to BMAA. Additionally, alchemical free energy results reveal that glutamate and the beta-carbamate adduct of BMAA have comparable binding affinity to the GluR2. These results provide a rationale that BMAA carbamate adducts may be, in fact, the modulators of GluR2 and not BMAA itself.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141436038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Small molecule antioxidants can inhibit or retard oxidation reactions and protect against free radical damage to cells, thus playing a key role in food, cosmetics, pharmaceuticals, the environment, as well as materials. Experimentally driven antioxidant discovery is a major paradigm, and computationally assisted antioxidants are rarely reported. In this study, a functional-group-based alternating multitask self-supervised molecular representation learning method is proposed to simultaneously predict the antioxidant activities of small molecules for eight commonly used in vitro antioxidant assays. Extensive evaluation results reveal that compared with the baseline models, the multitask FG-BERT model achieves the best overall predictive performance, with the highest average F1, BA, ROC-AUC, and PRC-AUC values of 0.860, 0.880, 0.954, and 0.937 for the test sets, respectively. The Y-scrambling testing results further demonstrate that such a deep learning model was not constructed by accident and that it has reliable predictive capabilities. Additionally, the excellent interpretability of the multitask FG-BERT model makes it easy to identify key structural fragments/groups that contribute significantly to the antioxidant effect of a given molecule. Finally, an online antioxidant activity prediction platform called AOP (freely available at https://aop.idruglab.cn/) and its local version were developed based on the high-quality multitask FG-BERT model for experts and nonexperts in the field. We anticipate that it will contribute to the discovery of novel small-molecule antioxidants.
{"title":"Highly Accurate and Explainable Predictions of Small-Molecule Antioxidants for Eight In Vitro Assays Simultaneously through an Alternating Multitask Learning Strategy.","authors":"Duancheng Zhao, Yanhong Zhang, Yihao Chen, Biaoshun Li, Wenguang Zhou, Ling Wang","doi":"10.1021/acs.jcim.4c00748","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00748","url":null,"abstract":"<p><p>Small molecule antioxidants can inhibit or retard oxidation reactions and protect against free radical damage to cells, thus playing a key role in food, cosmetics, pharmaceuticals, the environment, as well as materials. Experimentally driven antioxidant discovery is a major paradigm, and computationally assisted antioxidants are rarely reported. In this study, a functional-group-based alternating multitask self-supervised molecular representation learning method is proposed to simultaneously predict the antioxidant activities of small molecules for eight commonly used in vitro antioxidant assays. Extensive evaluation results reveal that compared with the baseline models, the multitask FG-BERT model achieves the best overall predictive performance, with the highest average F1, BA, ROC-AUC, and PRC-AUC values of 0.860, 0.880, 0.954, and 0.937 for the test sets, respectively. The Y-scrambling testing results further demonstrate that such a deep learning model was not constructed by accident and that it has reliable predictive capabilities. Additionally, the excellent interpretability of the multitask FG-BERT model makes it easy to identify key structural fragments/groups that contribute significantly to the antioxidant effect of a given molecule. Finally, an online antioxidant activity prediction platform called AOP (freely available at https://aop.idruglab.cn/) and its local version were developed based on the high-quality multitask FG-BERT model for experts and nonexperts in the field. We anticipate that it will contribute to the discovery of novel small-molecule antioxidants.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141416613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-17DOI: 10.1021/acs.jcim.4c00525
Yating Lin, Jun Xu, Qiong Gu
Ferroptosis is an iron-dependent programmed cell death characterized by lipid peroxidation that is linked to the pathophysiological processes in many diseases, such as neurodegenerative diseases, cancers, ischemia-reperfusion injuries, and organ damages. Many proteins are associated with ferroptosis signal transduction pathways. Novel chemical compounds are demanded to explore and regulate these pathways. Therefore, a ferroptosis ligand database, which holds relations among chemical structures, targets, bioactivities, and diseases, is needed for discovering and designing new ferroptosis regulators. This work reports FerroLigandDB, a manually curated database for small-molecular ferroptosis regulators. The database comprises 466 ferroptosis inducer entries (with 380 unique molecular structures) and 539 ferroptosis inhibitor entries (with 468 unique molecular structures) (note: one compound can be recorded as multiple entries due to the different assays). Each ferroptosis ligand entry is detailed with compound IDs, structure attributes, bioactivity values, test objects, target information, associated diseases, and references. The fields in the FerroLigandDB database implicitly contain relationships among chemical structures, bioactivities, targets, and diseases. Thus, FerroLigandDB is a comprehensive resource for scientists to design and discover novel ferroptosis regulators. The user interface of FerroLigandDB is implemented with query features and data visualization facilities. With compound identifiers, the compounds are linked to the records of other chemoinformatics databases (such as PubChem and SciFinder). The FerroLigandDB database is freely accessible at http://ferr.gulab.org.cn/.
{"title":"FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations.","authors":"Yating Lin, Jun Xu, Qiong Gu","doi":"10.1021/acs.jcim.4c00525","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00525","url":null,"abstract":"<p><p>Ferroptosis is an iron-dependent programmed cell death characterized by lipid peroxidation that is linked to the pathophysiological processes in many diseases, such as neurodegenerative diseases, cancers, ischemia-reperfusion injuries, and organ damages. Many proteins are associated with ferroptosis signal transduction pathways. Novel chemical compounds are demanded to explore and regulate these pathways. Therefore, a ferroptosis ligand database, which holds relations among chemical structures, targets, bioactivities, and diseases, is needed for discovering and designing new ferroptosis regulators. This work reports FerroLigandDB, a manually curated database for small-molecular ferroptosis regulators. The database comprises 466 ferroptosis inducer entries (with 380 unique molecular structures) and 539 ferroptosis inhibitor entries (with 468 unique molecular structures) (note: one compound can be recorded as multiple entries due to the different assays). Each ferroptosis ligand entry is detailed with compound IDs, structure attributes, bioactivity values, test objects, target information, associated diseases, and references. The fields in the FerroLigandDB database implicitly contain relationships among chemical structures, bioactivities, targets, and diseases. Thus, FerroLigandDB is a comprehensive resource for scientists to design and discover novel ferroptosis regulators. The user interface of FerroLigandDB is implemented with query features and data visualization facilities. With compound identifiers, the compounds are linked to the records of other chemoinformatics databases (such as PubChem and SciFinder). The FerroLigandDB database is freely accessible at http://ferr.gulab.org.cn/.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141416611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-14DOI: 10.1021/acs.jcim.4c00295
Sadik Bhattarai, Hilal Tayara, Kil To Chong
Anticancer peptides (ACPs) play a vital role in selectively targeting and eliminating cancer cells. Evaluating and comparing predictions from various machine learning (ML) and deep learning (DL) techniques is challenging but crucial for anticancer drug research. We conducted a comprehensive analysis of 15 ML and 10 DL models, including the models released after 2022, and found that support vector machines (SVMs) with feature combination and selection significantly enhance overall performance. DL models, especially convolutional neural networks (CNNs) with light gradient boosting machine (LGBM) based feature selection approaches, demonstrate improved characterization. Assessment using a new test data set (ACP10) identifies ACPred, MLACP 2.0, AI4ACP, mACPred, and AntiCP2.0_AAC as successive optimal predictors, showcasing robust performance. Our review underscores current prediction tool limitations and advocates for an omnidirectional ACP prediction framework to propel ongoing research.
{"title":"Advancing Peptide-Based Cancer Therapy with AI: In-Depth Analysis of State-of-the-Art AI Models.","authors":"Sadik Bhattarai, Hilal Tayara, Kil To Chong","doi":"10.1021/acs.jcim.4c00295","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00295","url":null,"abstract":"<p><p>Anticancer peptides (ACPs) play a vital role in selectively targeting and eliminating cancer cells. Evaluating and comparing predictions from various machine learning (ML) and deep learning (DL) techniques is challenging but crucial for anticancer drug research. We conducted a comprehensive analysis of 15 ML and 10 DL models, including the models released after 2022, and found that support vector machines (SVMs) with feature combination and selection significantly enhance overall performance. DL models, especially convolutional neural networks (CNNs) with light gradient boosting machine (LGBM) based feature selection approaches, demonstrate improved characterization. Assessment using a new test data set (ACP10) identifies ACPred, MLACP 2.0, AI4ACP, mACPred, and AntiCP2.0_AAC as successive optimal predictors, showcasing robust performance. Our review underscores current prediction tool limitations and advocates for an omnidirectional ACP prediction framework to propel ongoing research.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-14DOI: 10.1021/acs.jcim.4c00344
Christian Seitz, Surl-Hee Ahn, Haixin Wei, Matson Kyte, Gregory M Cook, Kurt L Krause, J Andrew McCammon
Discovered in the 1920s, cytochrome bd is a terminal oxidase that has received renewed attention as a drug target since its atomic structure was first determined in 2016. Only found in prokaryotes, we study it here as a drug target for Mycobacterium tuberculosis (Mtb). Most previous drug discovery efforts toward cytochrome bd have involved analogues of the canonical substrate quinone, known as Aurachin D. Here, we report six new cytochrome bd inhibitor scaffolds determined from a computational screen and confirmed on target activity through in vitro testing. These scaffolds provide new avenues for lead optimization toward Mtb therapeutics.
{"title":"Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome <i>bd</i> Oxidase.","authors":"Christian Seitz, Surl-Hee Ahn, Haixin Wei, Matson Kyte, Gregory M Cook, Kurt L Krause, J Andrew McCammon","doi":"10.1021/acs.jcim.4c00344","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00344","url":null,"abstract":"<p><p>Discovered in the 1920s, cytochrome <i>bd</i> is a terminal oxidase that has received renewed attention as a drug target since its atomic structure was first determined in 2016. Only found in prokaryotes, we study it here as a drug target for <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>). Most previous drug discovery efforts toward cytochrome <i>bd</i> have involved analogues of the canonical substrate quinone, known as Aurachin D. Here, we report six new cytochrome <i>bd</i> inhibitor scaffolds determined from a computational screen and confirmed on target activity through <i>in vitro</i> testing. These scaffolds provide new avenues for lead optimization toward <i>Mtb</i> therapeutics.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-13DOI: 10.1021/acs.jcim.4c00338
Leon Wehrhan, Bettina G. Keller
The serine protease trypsin forms a tightly bound inhibitor complex with the bovine pancreatic trypsin inhibitor (BPTI). The complex is stabilized by the P1 residue Lys15, which interacts with negatively charged amino acids at the bottom of the S1 pocket. Truncating the P1 residue of wildtype BPTI to α-aminobutyric acid (Abu) leaves a complex with moderate inhibitor strength, which is held in place by additional hydrogen bonds at the protein–protein interface. Fluorination of the Abu residue partially restores the inhibitor strength. The mechanism with which fluorination can restore the inhibitor strength is unknown, and accurate computational investigation requires knowledge of the binding and unbinding pathways. The preferred unbinding pathway is likely to be complex, as encounter states have been described before, and unrestrained umbrella sampling simulations of these complexes suggest additional energetic minima. Here, we use random acceleration molecular dynamics to find a new metastable state in the unbinding pathway of Abu-BPTI variants and wildtype BPTI from trypsin, which we call the prebound state. The prebound state and the fully bound state differ by a substantial shift in the position, a slight shift in the orientation of the BPTI variants, and changes in the interaction pattern. Particularly important is the breaking of three hydrogen bonds around Arg17. Fluorination of the P1 residue lowers the energy barrier of the transition between the fully bound state and prebound state and also lowers the energy minimum of the prebound state. While the effect of fluorination is in general difficult to quantify, here, it is in part caused by favorable stabilization of a hydrogen bond between Gln194 and Cys14. The interaction pattern of the prebound state offers insights into the inhibitory mechanism of BPTI and might add valuable information for the design of serine protease inhibitors.
{"title":"Prebound State Discovered in the Unbinding Pathway of Fluorinated Variants of the Trypsin–BPTI Complex Using Random Acceleration Molecular Dynamics Simulations","authors":"Leon Wehrhan, Bettina G. Keller","doi":"10.1021/acs.jcim.4c00338","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00338","url":null,"abstract":"The serine protease trypsin forms a tightly bound inhibitor complex with the bovine pancreatic trypsin inhibitor (BPTI). The complex is stabilized by the P1 residue Lys15, which interacts with negatively charged amino acids at the bottom of the S1 pocket. Truncating the P1 residue of wildtype BPTI to α-aminobutyric acid (Abu) leaves a complex with moderate inhibitor strength, which is held in place by additional hydrogen bonds at the protein–protein interface. Fluorination of the Abu residue partially restores the inhibitor strength. The mechanism with which fluorination can restore the inhibitor strength is unknown, and accurate computational investigation requires knowledge of the binding and unbinding pathways. The preferred unbinding pathway is likely to be complex, as encounter states have been described before, and unrestrained umbrella sampling simulations of these complexes suggest additional energetic minima. Here, we use random acceleration molecular dynamics to find a new metastable state in the unbinding pathway of Abu-BPTI variants and wildtype BPTI from trypsin, which we call the prebound state. The prebound state and the fully bound state differ by a substantial shift in the position, a slight shift in the orientation of the BPTI variants, and changes in the interaction pattern. Particularly important is the breaking of three hydrogen bonds around Arg17. Fluorination of the P1 residue lowers the energy barrier of the transition between the fully bound state and prebound state and also lowers the energy minimum of the prebound state. While the effect of fluorination is in general difficult to quantify, here, it is in part caused by favorable stabilization of a hydrogen bond between Gln194 and Cys14. The interaction pattern of the prebound state offers insights into the inhibitory mechanism of BPTI and might add valuable information for the design of serine protease inhibitors.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141315898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Optimization techniques play a pivotal role in advancing drug development, serving as the foundation of numerous generative methods tailored to efficiently design optimized molecules derived from existing lead compounds. However, existing methods often encounter difficulties in generating diverse, novel, and high-property molecules that simultaneously optimize multiple drug properties. To overcome this bottleneck, we propose a multiobjective molecule optimization framework (MOMO). MOMO employs a specially designed Pareto-based multiproperty evaluation strategy at the molecular sequence level to guide the evolutionary search in an implicit chemical space. A comparative analysis of MOMO with five state-of-the-art methods across two benchmark multiproperty molecule optimization tasks reveals that MOMO markedly outperforms them in terms of diversity, novelty, and optimized properties. The practical applicability of MOMO in drug discovery has also been validated on four challenging tasks in the real-world discovery problem. These results suggest that MOMO can provide a useful tool to facilitate molecule optimization problems with multiple properties.
{"title":"Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space.","authors":"Xin Xia, Yiping Liu, Chunhou Zheng, Xingyi Zhang, Qingwen Wu, Xin Gao, Xiangxiang Zeng, Yansen Su","doi":"10.1021/acs.jcim.4c00031","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00031","url":null,"abstract":"<p><p>Optimization techniques play a pivotal role in advancing drug development, serving as the foundation of numerous generative methods tailored to efficiently design optimized molecules derived from existing lead compounds. However, existing methods often encounter difficulties in generating diverse, novel, and high-property molecules that simultaneously optimize multiple drug properties. To overcome this bottleneck, we propose a multiobjective molecule optimization framework (MOMO). MOMO employs a specially designed Pareto-based multiproperty evaluation strategy at the molecular sequence level to guide the evolutionary search in an implicit chemical space. A comparative analysis of MOMO with five state-of-the-art methods across two benchmark multiproperty molecule optimization tasks reveals that MOMO markedly outperforms them in terms of diversity, novelty, and optimized properties. The practical applicability of MOMO in drug discovery has also been validated on four challenging tasks in the real-world discovery problem. These results suggest that MOMO can provide a useful tool to facilitate molecule optimization problems with multiple properties.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141316059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-13DOI: 10.1021/acs.jcim.4c00626
Bryan M Delfing, Xavier E Laracuente, William Jeffries, Xingyu Luo, Audrey Olson, Kenneth W Foreman, Greg Petruncio, Kyung Hyeon Lee, Mikell Paige, Kylene Kehn-Hall, Christopher Lockhart, Dmitri K Klimov
Venezuelan equine encephalitis virus (VEEV) is a highly virulent pathogen whose nuclear localization signal (NLS) sequence from capsid protein binds to the host importin-α transport protein and blocks nuclear import. We studied the molecular mechanisms by which two small ligands, termed I1 and I2, interfere with the binding of VEEV's NLS peptide to importin-α protein. To this end, we performed all-atom replica exchange molecular dynamics simulations probing the competitive binding of the VEEV coreNLS peptide and I1 or I2 ligand to the importin-α major NLS binding site. As a reference, we used our previous simulations, which examined noncompetitive binding of the coreNLS peptide or the inhibitors to importin-α. We found that both inhibitors completely abrogate the native binding of the coreNLS peptide, forcing it to adopt a manifold of nonnative loosely bound poses within the importin-α major NLS binding site. Both inhibitors primarily destabilize the native coreNLS binding by masking its amino acids rather than competing with it for binding to importin-α. Because I2, in contrast to I1, binds off-site localizing on the edge of the major NLS binding site, it inhibits fewer coreNLS native binding interactions than I1. Structural analysis is supported by computations of the free energies of the coreNLS peptide binding to importin-α with or without competition from the inhibitors. Specifically, both inhibitors reduce the free energy gain from coreNLS binding, with I1 causing significantly larger loss than I2. To test our simulations, we performed AlphaScreen experiments measuring IC50 values for both inhibitors. Consistent with in silico results, the IC50 value for I1 was found to be lower than that for I2. We hypothesize that the inhibitory action of I1 and I2 ligands might be specific to the NLS from VEEV's capsid protein.
{"title":"Competitive Binding of Viral Nuclear Localization Signal Peptide and Inhibitor Ligands to Importin-α Nuclear Transport Protein.","authors":"Bryan M Delfing, Xavier E Laracuente, William Jeffries, Xingyu Luo, Audrey Olson, Kenneth W Foreman, Greg Petruncio, Kyung Hyeon Lee, Mikell Paige, Kylene Kehn-Hall, Christopher Lockhart, Dmitri K Klimov","doi":"10.1021/acs.jcim.4c00626","DOIUrl":"https://doi.org/10.1021/acs.jcim.4c00626","url":null,"abstract":"<p><p>Venezuelan equine encephalitis virus (VEEV) is a highly virulent pathogen whose nuclear localization signal (NLS) sequence from capsid protein binds to the host importin-α transport protein and blocks nuclear import. We studied the molecular mechanisms by which two small ligands, termed I1 and I2, interfere with the binding of VEEV's NLS peptide to importin-α protein. To this end, we performed all-atom replica exchange molecular dynamics simulations probing the competitive binding of the VEEV coreNLS peptide and I1 or I2 ligand to the importin-α major NLS binding site. As a reference, we used our previous simulations, which examined noncompetitive binding of the coreNLS peptide or the inhibitors to importin-α. We found that both inhibitors completely abrogate the native binding of the coreNLS peptide, forcing it to adopt a manifold of nonnative loosely bound poses within the importin-α major NLS binding site. Both inhibitors primarily destabilize the native coreNLS binding by masking its amino acids rather than competing with it for binding to importin-α. Because I2, in contrast to I1, binds off-site localizing on the edge of the major NLS binding site, it inhibits fewer coreNLS native binding interactions than I1. Structural analysis is supported by computations of the free energies of the coreNLS peptide binding to importin-α with or without competition from the inhibitors. Specifically, both inhibitors reduce the free energy gain from coreNLS binding, with I1 causing significantly larger loss than I2. To test our simulations, we performed AlphaScreen experiments measuring IC50 values for both inhibitors. Consistent with in silico results, the IC50 value for I1 was found to be lower than that for I2. We hypothesize that the inhibitory action of I1 and I2 ligands might be specific to the NLS from VEEV's capsid protein.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141309546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}