Development and prospects of predicting drug polymorphs technology / 药学学报

Most chemical medicines have polymorphs. The difference of medicine polymorphs in physicochemical properties directly affects the stability, efficacy, and safety of solid medicine products. Polymorphs is incomparably important to pharmaceutical chemistry, manufacturing, and control. Meantime polymorphs is a key factor for the quality of high-end drug and formulations. Polymorph prediction technology can effectively guide screening of trial experiments, and reduce the risk of missing stable crystal form in the traditional experiment. Polymorph prediction technology was firstly based on theoretical calculations such as quantum mechanics and computational chemistry, and then was developed by the key technology of machine learning using the artificial intelligence. Nowadays, the popular trend is to combine the advantages of theoretical calculation and machine learning to jointly predict crystal structure. Recently, predicting medicine polymorphs has still been a challenging problem. It is expected to learn from and integrate existing technologies to predict medicine polymorphs more accurately and efficiently.

A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors

Protein arginine methyltransferases (PRMTs) are attractive targets for developing therapeutic agents, but selective PRMT inhibitors targeting the cofactor SAM binding site are limited. Herein, we report the discovery of a noncanonical but less polar SAH surrogate YD1113 by replacing the benzyl guanidine of a pan-PRMT inhibitor with a benzyl urea, potently and selectively inhibiting PRMT3/4/5. Importantly, crystal structures reveal that the benzyl urea moiety of YD1113 induces a unique and novel hydrophobic binding pocket in PRMT3/4, providing a structural basis for the selectivity. In addition, YD1113 can be modified by introducing a substrate mimic to form a "T-shaped" bisubstrate analogue YD1290 to engage both the SAM and substrate binding pockets, exhibiting potent and selective inhibition to type I PRMTs (IC50 < 5 nmol/L). In summary, we demonstrated the promise of YD1113 as a general SAH mimic to build potent and selective PRMT inhibitors.

P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate

WS9326A is a peptide antibiotic containing a highly unusual N-methyl-E-2-3-dehydrotyrosine (NMet-Dht) residue that is incorporated during peptide assembly on a non-ribosomal peptide synthetase (NRPS). The cytochrome P450 encoded by sas16 (P450Sas) has been shown to be essential for the formation of the alkene moiety in NMet-Dht, but the timing and mechanism of the P450Sas-mediated α,β-dehydrogenation of Dht remained unclear. Here, we show that the substrate of P450Sas is the NRPS-associated peptidyl carrier protein (PCP)-bound dipeptide intermediate (Z)-2-pent-1'-enyl-cinnamoyl-Thr-N-Me-Tyr. We demonstrate that P450Sas-mediated incorporation of the double bond follows N-methylation of the Tyr by the N-methyl transferase domain found within the NRPS, and further that P450Sas appears to be specific for substrates containing the (Z)-2-pent-1'-enyl-cinnamoyl group. A crystal structure of P450Sas reveals differences between P450Sas and other P450s involved in the modification of NRPS-associated substrates, including the substitution of the canonical active site alcohol residue with a phenylalanine (F250), which in turn is critical to P450Sas activity and WS9326A biosynthesis. Together, our results suggest that P450Sas catalyses the direct dehydrogenation of the NRPS-bound dipeptide substrate, thus expanding the repertoire of P450 enzymes that can be used to produce biologically active peptides.

Dihydrofolate reductase-like protein inactivates hemiaminal pharmacophore for self-resistance in safracin biosynthesis

Dihydrofolate reductase (DHFR), a housekeeping enzyme in primary metabolism, has been extensively studied as a model of acid-base catalysis and a clinic drug target. Herein, we investigated the enzymology of a DHFR-like protein SacH in safracin (SAC) biosynthesis, which reductively inactivates hemiaminal pharmacophore-containing biosynthetic intermediates and antibiotics for self-resistance. Furthermore, based on the crystal structure of SacH-NADPH-SAC-A ternary complexes and mutagenesis, we proposed a catalytic mechanism that is distinct from the previously characterized short-chain dehydrogenases/reductases-mediated inactivation of hemiaminal pharmacophore. These findings expand the functions of DHFR family proteins, reveal that the common reaction can be catalyzed by distinct family of enzymes, and imply the possibility for the discovery of novel antibiotics with hemiaminal pharmacophore.

Advances in the structure and function of chitosanase / 生物工程学报

Chitosanases represent a class of glycoside hydrolases with high catalytic activity on chitosan but nearly no activity on chitin. Chitosanases can convert high molecular weight chitosan into functional chitooligosaccharides with low molecular weight. In recent years, remarkable progress has been made in the research on chitosanases. This review summarizes and discusses its biochemical properties, crystal structures, catalytic mechanisms, and protein engineering, highlighting the preparation of pure chitooligosaccharides by enzymatic hydrolysis. This review may advance the understandings on the mechanism of chitosanases and promote its industrial applications.

Preparation, crystal structure and thermostability of nirmatrelvir polymorphs / 药学学报

The polymorphism and thermostability of nirmatrelvir, the main antiviral component of the oral COVID-19 treatment drug, were studied. Four polymorphs of nirmatrelvir were prepared by recrystallization methods. Among them, Form 1 and nirmatrelvir methyl tert-butyl ether solvate (Form 2) had been reported in the literature, while nirmatrelvir isobutyl acetate solvate (NMTW-IBAC) and nirmatrelvir ethyl acetate solvate (NMTW-EA) are two new solvates. The crystal structures were characterized by single-crystal X-ray diffraction, powder X-ray diffraction, thermogravimetric analysis and differential scanning calorimetry. The thermostability of polymorphism and crystalline transformation were also investigated by combining Hirshfeld surface analysis and interaction energy analysis. The results showed that nirmatrelvir Form 1 belongs orthorhombic crystal system with the space group P212121 and one nirmatrelvir molecule included in the asymmetric unit, which has the same crystal structure as nirmatrelvir Form 4 reported in the literature. Owing to its larger thermal expansion, the differences in crystallographic parameters obtained at different temperatures were found between Form 1 and Form 4. Three solvates of nirmatrelvir belonged to the iso-structural with monoclinic crystal system and the space group P21, in which the asymmetric unit contains one nirmatrelvir molecule and one solvent molecule. The thermal analysis results showed that nirmatrelvir Form 1 was a solvent-free crystal form with the best thermal stability and the strongest intermolecular hydrogen bonding. Among the three solvates, NMTW-EA has the worst thermal stability and the weakest hydrogen bonding interaction between the nirmatrelvir molecule and the solvent molecule. The energy framework of nirmatrelvir solvates showed that the closer the arrangement between solvent and nirmatrelvir molecules, the greater the total interaction energy between solvent and nirmatrelvir molecules. The phase transition studies of the three solvates showed that NMTW-IBAC and NMTW-EA were transformed into amorphous after desolvation, respectively, while Form 2 undergoes oiling during desolvation. The research provides theoretical guidance for the analysis, identification and quality control of nirmatrelvir polymorphs.

The Crystal Structure and Molecular Docking of CYP76AH3 in the Tanshinone Biosynthesis Pathway / 中国生物化学与分子生物学报

Salvia miltiorrhiza is widely used in the treatment of the angina pectoris, coronary heart disease and myocardial infarction. CYP76AH3 is the key P450 enzyme, locating at the branch point of the tanshinone synthesis pathway. The crystal structural study and key amino acid analysis are of great significance for synthetic biology study on tanshinone. But it is always a challenge for scientists to carry out protein purification, crystallization and crystal structural studies on transmembrane type Ⅱ P450 enzymes. In this study, the prokaryotic expression plasmid was generated, and the high-purity target protein was purified. CYP76AH3 was successfully crystallized, and the crystal structure was solved.After docking range was determined by Cavityplus analysis, molecular docking with Discovery Studio was conducted. The docking result indicated that Gly298 and Asp294 had hydrogen bond interaction with the substrate, while Phe479, Leu367 and Leu293 had hydrophobic interaction with the substrate.In addition, the effect of mutations at the key amino acids on the protein structure stability was predicted throung point mutation simulation. This study would provide a target for protein engineering of CYP76AH3 and lay a foundation for the study of synthesis biology on tanshinones.

Study of intermolecular interactions of piroxicam polymorphs / 药学学报

Piroxicam has polymorphism. Different crystalline forms can exhibit different physicochemical properties and biological activities. Analysis of the intermolecular interactions is essential to reveal the formation mechanism and differences of polymorphs. In this paper, Hirshfeld surface analysis and semi-empirical methods were used to calculate and analyze the intermolecular interactions in seven polymorphic forms of piroxicam. The results show that the Hirshfeld surface analysis method can clearly and intuitively reveal the intermolecular interactions, among which H…H, O…H/H…O and N…H/H…N interactions account for 95% of the total energy. There are differences in the proportion and distribution of the forces of different crystal forms. The energy calculation shows that the lattice energy of the hydrate is significantly lower than that of the anhydrous forms, and in the specific energy distribution, the contribution of the dispersion force is the most prominent. Further interaction energy analysis was found that within the distance of 3.8 Å from the center of the piroxicam molecule, different crystalline forms of piroxicam molecule have different interaction energies with surrounding molecules.

Function, structure and catalytic mechanism of sucrose phosphate synthase: a review / 生物工程学报

Sucrose is a natural product occurs widely in nature. In living organisms such as plants, sucrose phosphate synthase (SPS) is the key rate-limiting enzyme for sucrose synthesis. SPS catalyzes the synthesis of sucrose-6-phosphate, which is further hydrolyzed by sucrose phosphatase to form sucrose. Researches on SPS in recent decades have been focused on the determination of enzymatic activity of SPS, the identification of the inhibitors and activators of SPS, the covalent modification of SPS, the carbohydrate distribution in plants regulated by SPS, the mechanism for promoting plant growth by SPS, the sweetness of fruit controlled by SPS, and many others. A systematic review of these aspects as well as the crystal structure and catalytic mechanism of SPS are presented.

Research progress and thinking on improving physicochemical properties and efficacy of the active ingredients in traditional Chinese medicine based on crystal structure / 药学学报

The active ingredients in traditional Chinese medicine have been reported to possess significant pharmacological activity and played an important role in clinical treatments. However, lots of the active ingredients in traditional Chinese medicine suffer from disadvantages such as low solubility, high melting point and low stability that results in low bioavailability and limit its clinical application. Crystal structure plays an important role in improving physicochemical properties and efficacy of the active ingredients in traditional Chinese medicine. This review concludes the research advances of several crystal forms used in the active ingredients in traditional Chinese medicine in terms of polymorph, cocrystal, amorphous/coamorphous and nanocrystal. And the effects of crystal forms on the physicochemical properties and efficacy of the active ingredients in traditional Chinese medicine were reviewed. This research may be useful for the formulation preparation and development of the active ingredients in traditional Chinese medicine.

Research advances on stimulator of interferon genes (STING) and its agonists / 药学学报

As a key signal transduction molecule involved in the innate immune response, stimulator of interferon genes (STING) is triggered by cytosolic DNA from pathogen and host origins, and plays an important role in inducing the secretion of type I interferons and proinflammatory cytokines, thereby defending against viral and intracellular bacterial infections and regulating the production of spontaneous antitumor immune responses in vivo. Thus, STING agonists have shown useful therapeutic effects for pathogen infection and cancer. In the past decade research on STING and its agonists has progressed rapidly. Here, we summarize recent advances in the structure and activation of STING and the mechanism of the cGAS-STING pathway. In particular, we review research advances of STING agonists, analyze the crystal structure of STING in complex with its agonists and the structure-activity relationship of STING agonists, and summarize the strong challenges of developing STING agonists.

Crystal structure of SARS-CoV-2 papain-like protease

The pandemic of coronavirus disease 2019 (COVID-19) is changing the world like never before. This crisis is unlikely contained in the absence of effective therapeutics or vaccine. The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays essential roles in virus replication and immune evasion, presenting a charming drug target. Given the PLpro proteases of SARS-CoV-2 and SARS-CoV share significant homology, inhibitor developed for SARS-CoV PLpro is a promising starting point of therapeutic development. In this study, we sought to provide structural frameworks for PLpro inhibitor design. We determined the unliganded structure of SARS-CoV-2 PLpro mutant C111S, which shares many structural features of SARS-CoV PLpro. This crystal form has unique packing, high solvent content and reasonable resolution 2.5 Å, hence provides a good possibility for fragment-based screening using crystallographic approach. We characterized the protease activity of PLpro in cleaving synthetic peptide harboring nsp2/nsp3 juncture. We demonstrate that a potent SARS-CoV PLpro inhibitor GRL0617 is highly effective in inhibiting protease activity of SARS-CoV-2 with the IC

Structure-based engineering of PET hydrolase from Ideonella sakaiensis / 生物工程学报

Polyethylene terephthalate (PET) is a synthetic polymer consisting of ester bond-linked terephthalate and ethylene glycol. Tremendous amounts of PET have been produced and majority of them enters terrestrial and marine environment as wastes, posing serious threats to the global ecosystems. In 2016, a PET hydrolase from a PET-assimilating bacterium Ideonalla sakaiensis was reported and termed as IsPETase. This enzyme outperforms other PET-hydrolyzing enzymes in terms of its PET hydrolytic activity at ambient temperature, thus holds a great promise for PET biodegradation. In order to improve IsPETase activity, we conducted structure-based engineering to modify the putative substrate-binding tunnel. Among the several variants to the N233 residue of IsPETase, we discovered that the substitution of N233 with alanine increases its PET hydrolytic activity, which can be further enhanced when combined with a R280A mutation. We also determined the X-ray crystal structure of the IsPETase N233A variant, which shares nearly identical fold to the WT protein, except for an open end of subsite Ⅱ. We hypothesized that the smaller side chain of N233A variant might lead to an extended subsite Ⅱ for PET binding, which subsequently increases the enzymatic activity. Thus, this study provides new clues for further structure-based engineering of PETase.

Discovery of highly selective and orally available benzimidazole-based phosphodiesterase 10 inhibitors with improved solubility and pharmacokinetic properties for treatment of pulmonary arterial hypertension

Optimization efforts were devoted to discover novel PDE10A inhibitors in order to improve solubility and pharmacokinetics properties for a long-term therapy against pulmonary arterial hypertension (PAH) starting from the previously synthesized inhibitor

Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites

The outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 virus continually lead to worldwide human infections and deaths. Currently, there is no specific viral protein-targeted therapeutics. Viral nucleocapsid protein is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. However, the structural information of SARS-CoV-2 nucleocapsid protein remains unclear. Herein, we have determined the 2.7 Å crystal structure of the N-terminal RNA binding domain of SARS-CoV-2 nucleocapsid protein. Although the overall structure is similar as other reported coronavirus nucleocapsid protein N-terminal domain, the surface electrostatic potential characteristics between them are distinct. Further comparison with mild virus type HCoV-OC43 equivalent domain demonstrates a unique potential RNA binding pocket alongside the -sheet core. Complemented by binding studies, our data provide several atomic resolution features of SARS-CoV-2 nucleocapsid protein N-terminal domain, guiding the design of novel antiviral agents specific targeting to SARS-CoV-2.

Research progress in structure and function of pectin methylesterase / 生物工程学报

Pectin methylesterase (PME) is an important pectinase that hydrolyzes methyl esters in pectin to release methanol and reduce the degree of methylation of pectin. At present, it has broad application prospects in food processing, tea beverage, paper making and other production processes. With the in-depth study of PME, the crystal structures with different sources have been reported. Analysis of these resolved crystal structures reveals that PME belongs to the right-hand parallel β-helix structure, and its catalytic residues are two aspartic acids and a glutamine, which play the role of general acid-base, nucleophile and stable intermediate, in the catalytic process. At the same time, the substrate specificity is analyzed to understand the recognition mechanism of the substrate and active sites. This paper systematically reviews these related aspects.

Synthesis, characterization, X-ray crystal structure and DFT calculations of 4-([2,2':6',2 '' -terpyridin]-4'-yl)phenol / Síntesis, caracterización, estructura cristalina y cálculos DFT para el 4-([2,2':6',2 '' -terpiridin]-4'-il)fenol / Síntese, caracterização, estrutura de cristal e cálculos DFT para o 4-([2,2':6',2 '' -terpiridina]-4'-il)fenol

Abstract The synthesis of new terpyridine (Tpy) derivatives has been subject of extensive research due to its potential as functional materials for solar energy conversion, among other applications. In this contribution, the 4-([2,2':6',2"-terpyndm]-4'-yl)phenol (TpyOH) was synthesized, characterized and studied through several methods, including X-ray crystallography and computational approaches. Single crystal X-ray structure analysis shows that TpyOH is essentially planar, with dihedral angles of about 5.03° between the central pyridinyl and the phenolic ring, and also 6.05 and 12.2° in the terpyridine moiety. In the crystal, molecules are linked by intermolecular hydrogen bonds and through П- П stacking interactions. Using a time dependent density functional theory approach and taking into account bulk solvent effects, the absorption and fluorescence spectra of TpyOH were investigated and compared. The TD-DFT S0→Sn and S1 →S0 transition energies are in good agreement with experimental results. The frontier molecular orbitals analysis showed that the low-energy absorption band has an intraligand charge transfer character (ICT), while the high-energy band is a common feature of П- П* transitions of the Tpy moiety. The S1→S0 emission transition also has an ICT character, with a 90% contribution from the HOMO→LUMO transitions.

Resumen La síntesis de derivados terpiridinicos (Tpy) se ha investigado ampliamente debido a su potencial para la conversión de energía solar En este artículo se sintetizó y caracterizó el 4-([2,2':6',2"-terpiridin]-4'-il)fenol (TpyOH), a través de varias metodologías como la cristalografía de rayos X y herramientas computacionales. El análisis de rayos X de monocristal mostró que el TpyOH es plano, con ángulos diedros de 5,03° entre el piridinilo central y el anillo fenólico, con presencia de ángulos de 6,05 y 12,2° en la porción terpiridínica. En el cristal, las moléculas están unidas por enlaces de hidrógeno intermoleculares y mediante interacciones de apilamiento n-n. Utilizando cálculos DFT dependientes del tiempo (TD-DFT) y teniendo en cuenta el efecto de los disolventes, se investigaron y compararon los espectros de absorción y fluorescencia de TpyOH. Las energías de transición TD-DFT de S0→Sn y S1→S0 concuerdan con los resultados experimentales. El análisis de orbitales moleculares de frontera mostró que la banda de absorción de baja energía corresponde a transferencia de carga intraligando (ICT); mientras que la banda de alta energía es común en las transiciones П-П* del resto Tpy. La emisión debido a la transición S1→S0 corresponde a ICT, con una contribución del 90% proveniente de transiciones HOMO→LUMO.

Resumo A síntese de derivados de terpiridina (Tpy) tem sido estudada devido ao seu potencial para a conversão de energia solar. Nesta contribuição, o 4-([2,2':6',2"- terpindina]-4'-il) fenol (TpyOH) foi sintetizado, caracterizado e estudado por vários métodos A análise de estrutura de raios X de cristal único mostra que o TpyOH é plano, com Ångulos diedros de 5,03 ° entre o piridinilo central e o anel fenólico, e também 6,05 e 12,2 ° na porção de terpiridina No cristal, as moléculas são ligadas por ligações intermoleculares de hidrogênio e através de interações de empilhamento n-n. Usando uma abordagem da teoria funcional da densidade dependente do tempo e levando em consideração os efeitos do solvente em massa, foram investigados e comparados os espectros de absorção e fluorescência do TpyOH As energias de transição TD-DFT S0→Sn e S1→S0 estão de acordo com os resultados experimentais A análise de orbitários moleculares de fronteira mostrou que a banda de absorção de baixa energia possui um caráter de transferência de carga intraligando (TIC), enquanto a banda de alta energia é uma característica comum das transições П-П* da fração Tpy. A transição de emissão S1→S0 também tem um caráter TIC, com uma contribuição de 90% das transições HOMO→LUMO.

Ethyl Haematommate from Stereocaulon graminosum Schaer.: Isolation and Crystal Structure

Herein, we reported the phytochemical investigation of whole thallus Sumatran lichen, Stereocaulon graminosum Schaer, and isolated a mono aromatic compound, ethyl haematommate (1). The structure of compound 1 have been established based on spectroscopic data and confirmed by single crystal X-ray structure analysis.

Insights into structure and function of diterpene synthases in plants / 药学学报

Diterpene synthases from plants are key enzymes in diterpene biosynthesis, which catalyzed the initial cyclization cascade of (E,E,E,)-geranylgeranyl pyrophosphate, and generated diverse carbon skeletons. Recent research show that the structural and stereo chemical differences lead to diverse natural diterpene compounds of plants. The structures of diterpene synthases play a crucial role in cyclization function. This article mainly reviews the mechanisms, functional characteristics, and structural information of diterpene synthases according to the crystal structures and functions.

Effect of sumoylation on the structure and activity of human thymine DNA glycosylase / 上海交通大学学报（医学版）

Objective: To study the effect of sumoylation on the structure, stability and activity of human thymine DNA glycosylase (TDG). Methods: Expression and purification systems were established for obtaining SUMO-1-TDG protein with high purity which can be used for crystal screening and activity detection. Structure of SUMO-1-TDG was solved after crystal screening, diffraction data collection and structure analysis. The change of TDG stability led by sumoylation was detected through a protein thermal shift assay. In addition, an activity assay was applied to investigate the effect of sumoylation on the activity of TDG. Results: A high-resolution structure of SUMO-1-TDG which could clearly describe the interaction between TDG and SUMO-1 was solved. The melting temperature (Tm) value of SUMO-1-TDG increased by about 16℃ and the catalytic activity increased by 9.70%, comparing with TDG protein. Conclusion: SUMO-1 binds to TDG to modify the intermolecular interaction of amino acids near the binding site, and further participates in the regulation of the stability and catalytic activity of TDG protein.