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1.
Nature ; 620(7973): 434-444, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37468638

ABSTRACT

Advances in DNA sequencing and machine learning are providing insights into protein sequences and structures on an enormous scale1. However, the energetics driving folding are invisible in these structures and remain largely unknown2. The hidden thermodynamics of folding can drive disease3,4, shape protein evolution5-7 and guide protein engineering8-10, and new approaches are needed to reveal these thermodynamics for every sequence and structure. Here we present cDNA display proteolysis, a method for measuring thermodynamic folding stability for up to 900,000 protein domains in a one-week experiment. From 1.8 million measurements in total, we curated a set of around 776,000 high-quality folding stabilities covering all single amino acid variants and selected double mutants of 331 natural and 148 de novo designed protein domains 40-72 amino acids in length. Using this extensive dataset, we quantified (1) environmental factors influencing amino acid fitness, (2) thermodynamic couplings (including unexpected interactions) between protein sites, and (3) the global divergence between evolutionary amino acid usage and protein folding stability. We also examined how our approach could identify stability determinants in designed proteins and evaluate design methods. The cDNA display proteolysis method is fast, accurate and uniquely scalable, and promises to reveal the quantitative rules for how amino acid sequences encode folding stability.


Subject(s)
Biology , Protein Engineering , Protein Folding , Proteins , Amino Acids/genetics , Amino Acids/metabolism , Biology/methods , DNA, Complementary/genetics , Protein Stability , Proteins/chemistry , Proteins/genetics , Proteins/metabolism , Thermodynamics , Proteolysis , Protein Engineering/methods , Protein Domains/genetics , Mutation
2.
Plant Biotechnol J ; 21(4): 698-710, 2023 04.
Article in English | MEDLINE | ID: mdl-36529909

ABSTRACT

Although plant secondary metabolites are important source of new drugs, obtaining these compounds is challenging due to their high structural diversity and low abundance. The roots of Astragalus membranaceus are a popular herbal medicine worldwide. It contains a series of cycloartane-type saponins (astragalosides) as hepatoprotective and antivirus components. However, astragalosides exhibit complex sugar substitution patterns which hindered their purification and bioactivity investigation. In this work, glycosyltransferases (GT) from A. membranaceus were studied to synthesize structurally diverse astragalosides. Three new GTs, AmGT1/5 and AmGT9, were characterized as 3-O-glycosyltransferase and 25-O-glycosyltransferase of cycloastragenol respectively. AmGT1G146V/I variants were obtained as specific 3-O-xylosyltransferases by sequence alignment, molecular modelling and site-directed mutagenesis. A combinatorial synthesis system was established using AmGT1/5/9, AmGT1G146V/S and the reported AmGT8 and AmGT8A394F . The system allowed the synthesis of 13 astragalosides in Astragalus root with conversion rates from 22.6% to 98.7%, covering most of the sugar-substitution patterns for astragalosides. In addition, AmGT1 exhibited remarkable sugar donor promiscuity to use 10 different donors, and was used to synthesize three novel astragalosides and ginsenosides. Glycosylation remarkably improved the hepatoprotective and SARS-CoV-2 inhibition activities for triterpenoids. This is one of the first attempts to produce a series of herbal constituents via combinatorial synthesis. The results provided new biocatalytic tools for saponin biosynthesis.


Subject(s)
COVID-19 , Plants, Medicinal , Saponins , Triterpenes , Astragalus propinquus/chemistry , Astragalus propinquus/genetics , Astragalus propinquus/metabolism , Saponins/chemistry , Saponins/metabolism , Glycosyltransferases/genetics , SARS-CoV-2 , Triterpenes/metabolism , Protein Engineering , Sugars/metabolism
3.
Science ; 376(6599): 1321-1327, 2022 06 17.
Article in English | MEDLINE | ID: mdl-35709255

ABSTRACT

The emergence of new therapeutic modalities requires complementary tools for their efficient syntheses. Availability of methodologies for site-selective modification of biomolecules remains a long-standing challenge, given the inherent complexity and the presence of repeating residues that bear functional groups with similar reactivity profiles. We describe a bioconjugation strategy for modification of native peptides relying on high site selectivity conveyed by enzymes. We engineered penicillin G acylases to distinguish among free amino moieties of insulin (two at amino termini and an internal lysine) and manipulate cleavable phenylacetamide groups in a programmable manner to form protected insulin derivatives. This enables selective and specific chemical ligation to synthesize homogeneous bioconjugates, improving yield and purity compared to the existing methods, and generally opens avenues in the functionalization of native proteins to access biological probes or drugs.


Subject(s)
Insulin , Penicillin Amidase , Peptides , Protein Engineering , Amino Acid Sequence , Humans , Insulin/analogs & derivatives , Insulin/biosynthesis , Lysine/chemistry , Penicillin Amidase/chemistry , Penicillin Amidase/genetics , Peptides/chemistry , Peptides/genetics , Protein Engineering/methods
4.
Int J Mol Sci ; 23(6)2022 Mar 08.
Article in English | MEDLINE | ID: mdl-35328351

ABSTRACT

Nanobodies provide important advantages over traditional antibodies, including their smaller size and robust biochemical properties such as high thermal stability, high solubility, and the ability to be bioengineered into novel multivalent, multi-specific, and high-affinity molecules, making them a class of emerging powerful therapies against SARS-CoV-2. Recent research efforts on the design, protein engineering, and structure-functional characterization of nanobodies and their binding with SARS-CoV-2 S proteins reflected a growing realization that nanobody combinations can exploit distinct binding epitopes and leverage the intrinsic plasticity of the conformational landscape for the SARS-CoV-2 S protein to produce efficient neutralizing and mutation resistant characteristics. Structural and computational studies have also been instrumental in quantifying the structure, dynamics, and energetics of the SARS-CoV-2 spike protein binding with nanobodies. In this review, a comprehensive analysis of the current structural, biophysical, and computational biology investigations of SARS-CoV-2 S proteins and their complexes with distinct classes of nanobodies targeting different binding sites is presented. The analysis of computational studies is supplemented by an in-depth examination of mutational scanning simulations and identification of binding energy hotspots for distinct nanobody classes. The review is focused on the analysis of mechanisms underlying synergistic binding of multivalent nanobodies that can be superior to single nanobodies and conventional nanobody cocktails in combating escape mutations by effectively leveraging binding avidity and allosteric cooperativity. We discuss how structural insights and protein engineering approaches together with computational biology tools can aid in the rational design of synergistic combinations that exhibit superior binding and neutralization characteristics owing to avidity-mediated mechanisms.


Subject(s)
Binding Sites , Molecular Docking Simulation , Molecular Dynamics Simulation , Single-Domain Antibodies/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Amino Acids , Antibody Affinity , Epitopes/chemistry , Epitopes/metabolism , Humans , Multiprotein Complexes/chemistry , Mutagenesis , Protein Binding , Protein Engineering , Protein Interaction Domains and Motifs , Single-Domain Antibodies/genetics , Single-Domain Antibodies/metabolism , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism
5.
Angew Chem Int Ed Engl ; 61(8): e202113587, 2022 02 14.
Article in English | MEDLINE | ID: mdl-34894044

ABSTRACT

Engineering the function of triterpene glucosyltransferases (GTs) is challenging due to the large size of the sugar acceptors. In this work, we identified a multifunctional glycosyltransferase AmGT8 catalyzing triterpene 3-/6-/2'-O-glycosylation from the medicinal plant Astragalus membranaceus. To engineer its regiospecificity, a small mutant library was built based on semi-rational design. Variants A394F, A394D, and T131V were found to catalyze specific 6-O, 3-O, and 2'-O glycosylation, respectively. The origin of regioselectivity of AmGT8 and its A394F variant was studied by molecular dynamics and hydrogen deuterium exchange mass spectrometry. Residue 394 is highly conserved as A/G and is critical for the regiospecificity of the C- and O-GTs TcCGT1 and GuGT10/14. Finally, astragalosides III and IV were synthesized by mutants A394F, T131V and P192E. This work reports biocatalysts for saponin synthesis and gives new insights into protein engineering of regioselectivity in plant GTs.


Subject(s)
Glycosyltransferases/metabolism , Protein Engineering , Saponins/biosynthesis , Triterpenes/metabolism , Astragalus propinquus/enzymology , Biocatalysis , Glycosyltransferases/chemistry , Protein Conformation , Saponins/chemistry , Stereoisomerism , Triterpenes/chemistry
6.
Int J Biol Macromol ; 196: 151-162, 2022 Jan 31.
Article in English | MEDLINE | ID: mdl-34920062

ABSTRACT

Arginine deiminase is a well-recognized guanidino-modifying hydrolase that catalyzes the conversion of L-arginine to citrulline and ammonia. Their biopotential to regress tumors via amino acid deprivation therapy (AADT) has been well established. PEGylated formulation of recombinant Mycoplasma ADI is in the last-phase clinical trials against various arginine-auxotrophic cancers like hepatocellular carcinoma, melanoma, and mesothelioma. Recently, ADIs have attained immense importance in several other biomedical applications, namely treatment of Alzheimer's, as an antiviral drug, bioproduction of nutraceutical L-citrulline and bio-analytics involving L-arginine detection. Considering the wide applications of this biodrug, the demand for ADI is expected to escalate several-fold in the coming years. However, the sustainable production aspects of the enzyme with improved pharmacokinetics is still limited, creating bottlenecks for effective biopharmaceutical development. To circumvent the lacunae in enzyme production with appropriate paradigms of 'quality-by-design' an explicit overview of its properties with 'biobetter' formulations strategies are required. Present review provides an insight into all the potential biomedical applications of ADI along with the improvements required for its reach to clinics. Recent research advances with special emphasis on the development of ADI as a 'biobetter' enzyme have also been comprehensively elaborated.


Subject(s)
Drug Development , Hydrolases/chemistry , Hydrolases/pharmacology , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Bacterial Proteins/chemistry , Bacterial Proteins/pharmacology , Biomedical Research , Biomedical Technology , Catalysis , Clinical Trials as Topic , Drug Evaluation, Preclinical , Fungal Proteins/chemistry , Fungal Proteins/pharmacology , Humans , Metabolic Networks and Pathways , Protein Engineering , Structure-Activity Relationship
7.
Proc Natl Acad Sci U S A ; 118(51)2021 12 21.
Article in English | MEDLINE | ID: mdl-34903659

ABSTRACT

Benzylisoquinoline alkaloids (BIAs) are a diverse class of medicinal plant natural products. Nearly 500 dimeric bisbenzylisoquinoline alkaloids (bisBIAs), produced by the coupling of two BIA monomers, have been characterized and display a range of pharmacological properties, including anti-inflammatory, antitumor, and antiarrhythmic activities. In recent years, microbial platforms have been engineered to produce several classes of BIAs, which are rare or difficult to obtain from natural plant hosts, including protoberberines, morphinans, and phthalideisoquinolines. However, the heterologous biosyntheses of bisBIAs have thus far been largely unexplored. Here, we describe the engineering of yeast strains that produce the Type I bisBIAs guattegaumerine and berbamunine de novo. Through strain engineering, protein engineering, and optimization of growth conditions, a 10,000-fold improvement in the production of guattegaumerine, the major bisBIA pathway product, was observed. By replacing the cytochrome P450 used in the final coupling reaction with a chimeric variant, the product profile was inverted to instead produce solely berbamunine. Our highest titer engineered yeast strains produced 108 and 25 mg/L of guattegaumerine and berbamunine, respectively. Finally, the inclusion of two additional putative BIA biosynthesis enzymes, SiCNMT2 and NnOMT5, into our bisBIA biosynthetic strains enabled the production of two derivatives of bisBIA pathway intermediates de novo: magnocurarine and armepavine. The de novo heterologous biosyntheses of bisBIAs presented here provide the foundation for the production of additional medicinal bisBIAs in yeast.


Subject(s)
Benzylisoquinolines/metabolism , Isoquinolines/metabolism , Saccharomyces cerevisiae/metabolism , Alkaloids/biosynthesis , Biosynthetic Pathways , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , Fermentation , Metabolic Engineering , Plant Proteins/genetics , Plant Proteins/metabolism , Protein Engineering , Racemases and Epimerases/genetics , Racemases and Epimerases/metabolism , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Saccharomyces cerevisiae/genetics , Tetrahydroisoquinolines/chemistry , Tetrahydroisoquinolines/metabolism
8.
Proc Natl Acad Sci U S A ; 118(45)2021 11 09.
Article in English | MEDLINE | ID: mdl-34740972

ABSTRACT

Serine proteases are essential for many physiological processes and require tight regulation by serine protease inhibitors (SERPINs). A disturbed SERPIN-protease balance may result in disease. The reactive center loop (RCL) contains an enzymatic cleavage site between the P1 through P1' residues that controls SERPIN specificity. This RCL can be modified to improve SERPIN function; however, a lack of insight into sequence-function relationships limits SERPIN development. This is complicated by more than 25 billion mutants needed to screen the entire P4 to P4' region. Here, we developed a platform to predict the effects of RCL mutagenesis by using α1-antitrypsin as a model SERPIN. We generated variants for each of the residues in P4 to P4' region, mutating them into each of the 20 naturally occurring amino acids. Subsequently, we profiled the reactivity of the resulting 160 variants against seven proteases involved in coagulation. These profiles formed the basis of an in silico prediction platform for SERPIN inhibitory behavior with combined P4 to P4' RCL mutations, which were validated experimentally. This prediction platform accurately predicted SERPIN behavior against five out of the seven screened proteases, one of which was activated protein C (APC). Using these findings, a next-generation APC-inhibiting α1-antitrypsin variant was designed (KMPR/RIRA; / indicates the cleavage site). This variant attenuates blood loss in an in vivo hemophilia A model at a lower dosage than the previously developed variant AIKR/KIPP because of improved potency and specificity. We propose that this SERPIN-based RCL mutagenesis approach improves our understanding of SERPIN behavior and will facilitate the design of therapeutic SERPINs.


Subject(s)
Drug Design , Models, Molecular , Protein C Inhibitor/genetics , Protein Engineering , alpha 1-Antitrypsin/genetics , Animals , Blood Coagulation Tests , Drug Evaluation, Preclinical , HEK293 Cells , Hemophilia A/drug therapy , Humans , Mice , Protein C Inhibitor/metabolism , Protein C Inhibitor/therapeutic use , Substrate Specificity , alpha 1-Antitrypsin/metabolism , alpha 1-Antitrypsin/therapeutic use
9.
Front Immunol ; 12: 737973, 2021.
Article in English | MEDLINE | ID: mdl-34691043

ABSTRACT

Influenza virus alters glycosylation patterns on its surface exposed glycoproteins to evade host adaptive immune responses. The viral hemagglutinin (HA), in particular the H3 subtype, has increased its overall surface glycosylation since its introduction in 1968. We previously showed that modulating predicted N-linked glycosylation sites on H3 A/Hong Kong/1/1968 HA identified a conserved epitope at the HA interface. This epitope is occluded on the native HA trimer but is likely exposed during HA "breathing" on the virion surface. Antibodies directed to this site are protective via an ADCC-mediated mechanism. This glycan engineering strategy made an otherwise subdominant epitope dominant in the murine model. Here, we asked whether cysteine stabilization of the hyperglycosylated HA trimer could reverse this immunodominance by preventing access to the interface epitope and focus responses to the HA receptor binding site (RBS). While analysis of serum responses from immunized mice did not show a redirection to the RBS, cysteine stabilization did result in an overall reduction in immunogenicity of the interface epitope. Thus, glycan engineering and cysteine stabilization are two strategies that can be used together to alter immunodominance patterns to HA. These results add to rational immunogen design approaches used to manipulate immune responses for the development of next-generation influenza vaccines.


Subject(s)
Antibodies, Neutralizing/blood , Hemagglutinin Glycoproteins, Influenza Virus/administration & dosage , Immunogenicity, Vaccine , Influenza Vaccines/administration & dosage , Animals , Cysteine , Female , Glycosylation , HEK293 Cells , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Humans , Immunity, Humoral , Immunization , Immunodominant Epitopes , Influenza Vaccines/genetics , Influenza Vaccines/immunology , Mice, Inbred C57BL , Protein Engineering
10.
Nat Commun ; 12(1): 6215, 2021 10 28.
Article in English | MEDLINE | ID: mdl-34711827

ABSTRACT

In phenylketonuria (PKU) patients, a genetic defect in the enzyme phenylalanine hydroxylase (PAH) leads to elevated systemic phenylalanine (Phe), which can result in severe neurological impairment. As a treatment for PKU, Escherichia coli Nissle (EcN) strain SYNB1618 was developed under Synlogic's Synthetic Biotic™ platform to degrade Phe from within the gastrointestinal (GI) tract. This clinical-stage engineered strain expresses the Phe-metabolizing enzyme phenylalanine ammonia lyase (PAL), catalyzing the deamination of Phe to the non-toxic product trans-cinnamate (TCA). In the present work, we generate a more potent EcN-based PKU strain through optimization of whole cell PAL activity, using biosensor-based high-throughput screening of mutant PAL libraries. A lead enzyme candidate from this screen is used in the construction of SYNB1934, a chromosomally integrated strain containing the additional Phe-metabolizing and biosafety features found in SYNB1618. Head-to-head, SYNB1934 demonstrates an approximate two-fold increase in in vivo PAL activity compared to SYNB1618.


Subject(s)
Biological Therapy , Escherichia coli Proteins/genetics , Escherichia coli/enzymology , Phenylalanine Ammonia-Lyase/genetics , Phenylalanine/metabolism , Phenylketonurias/metabolism , Phenylketonurias/therapy , Biosensing Techniques , Cinnamates , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Humans , Phenylalanine Ammonia-Lyase/metabolism , Protein Engineering
11.
Microb Cell Fact ; 20(1): 170, 2021 Aug 28.
Article in English | MEDLINE | ID: mdl-34454478

ABSTRACT

BACKGROUND: Melatonin has attracted substantial attention because of its excellent prospects for both medical applications and crop improvement. The microbial production of melatonin is a safer and more promising alternative to chemical synthesis approaches. Researchers have failed to produce high yields of melatonin in common heterologous hosts due to either the insolubility or low enzyme activity of proteins encoded by gene clusters related to melatonin biosynthesis. RESULTS: Here, a combinatorial gene pathway for melatonin production was successfully established in Escherichia coli by combining the physostigmine biosynthetic genes from Streptomyces albulus and gene encoding phenylalanine 4-hydroxylase (P4H) from Xanthomonas campestris and caffeic acid 3-O-methyltransferase (COMT) from Oryza sativa. A threefold improvement of melatonin production was achieved by balancing the expression of heterologous proteins and adding 3% glycerol. Further protein engineering and metabolic engineering were conducted to improve the conversion of N-acetylserotonin (NAS) to melatonin. Construction of COMT variant containing C303F and V321T mutations increased the production of melatonin by fivefold. Moreover, the deletion of speD gene increased the supply of S-adenosylmethionine (SAM), an indispensable cofactor of COMT, which doubled the yield of melatonin. In the final engineered strain EcMEL8, the production of NAS and melatonin reached 879.38 ± 71.42 mg/L and 136.17 ± 1.33 mg/L in a shake flask. Finally, in a 2-L bioreactor, EcMEL8 produced 1.06 ± 0.07 g/L NAS and 0.65 ± 0.11 g/L melatonin with tryptophan supplementation. CONCLUSIONS: This study established a novel combinatorial pathway for melatonin biosynthesis in E. coli and provided alternative strategies for improvement of melatonin production.


Subject(s)
Escherichia coli/metabolism , Melatonin/biosynthesis , Metabolic Engineering/methods , Protein Engineering/methods , Escherichia coli/genetics
12.
Int J Mol Sci ; 22(13)2021 Jun 22.
Article in English | MEDLINE | ID: mdl-34206616

ABSTRACT

The biophysical properties of therapeutic antibodies influence their manufacturability, efficacy, and safety. To develop an anti-cancer antibody, we previously generated a human monoclonal antibody (Ab417) that specifically binds to L1 cell adhesion molecule with a high affinity, and we validated its anti-tumor activity and mechanism of action in human cholangiocarcinoma xenograft models. In the present study, we aimed to improve the biophysical properties of Ab417. We designed 20 variants of Ab417 with reduced aggregation propensity, less potential post-translational modification (PTM) motifs, and the lowest predicted immunogenicity using computational methods. Next, we constructed these variants to analyze their expression levels and antigen-binding activities. One variant (Ab612)-which contains six substitutions for reduced surface hydrophobicity, removal of PTM, and change to the germline residue-exhibited an increased expression level and antigen-binding activity compared to Ab417. In further studies, compared to Ab417, Ab612 showed improved biophysical properties, including reduced aggregation propensity, increased stability, higher purification yield, lower pI, higher affinity, and greater in vivo anti-tumor efficacy. Additionally, we generated a highly productive and stable research cell bank (RCB) and scaled up the production process to 50 L, yielding 6.6 g/L of Ab612. The RCB will be used for preclinical development of Ab612.


Subject(s)
Antibodies, Monoclonal/chemistry , Models, Molecular , Neural Cell Adhesion Molecule L1/chemistry , Protein Engineering , Animals , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/pharmacology , Antibody Affinity , CHO Cells , Chemical Phenomena , Cricetulus , Drug Design , Drug Evaluation, Preclinical , Humans , Neural Cell Adhesion Molecule L1/antagonists & inhibitors , Protein Engineering/methods , Protein Stability , Thermodynamics
13.
Curr Issues Mol Biol ; 43(2): 687-703, 2021 Jul 13.
Article in English | MEDLINE | ID: mdl-34287263

ABSTRACT

Cellulases have been used to extract bioactive ingredients from medical plants; however, the poor enzymatic properties of current cellulases significantly limit their application. Two strategies are expected to address this concern: (1) new cellulase gene mining strategies have been promoted, optimized, and integrated, thanks to the improvement of gene sequencing, genomic data, and algorithm optimization, and (2) known cellulases are being modified, thanks to the development of protein engineering, crystal structure data, and computing power. Here, we focus on mining strategies and provide a systemic overview of two approaches based on sequencing and function. Strategies based on protein structure modification, such as introducing disulfide bonds, proline, salt bridges, N-glycosylation modification, and truncation of loop structures, have already been summarized. This review discusses four aspects of cellulase-assisted extraction. Initially, cellulase alone was used to extract bioactive substances, and later, mixed enzyme systems were developed. Physical methods such as ultrasound, microwave, and high hydrostatic pressure have assisted in improving extraction efficiency. Cellulase changes the structure of biomolecules during the extraction process to convert them into effective ingredients with better activity and bioavailability. The combination of cellulase with other enzymes and physical technologies is a promising strategy for future extraction applications.


Subject(s)
Cellulases/chemistry , Data Mining , Protein Engineering , Cellulases/genetics , Cellulases/isolation & purification , Cellulases/metabolism , Chemical Fractionation/methods , Computational Biology/methods , Data Mining/methods , Enzyme Stability , Plant Extracts/chemistry , Plant Extracts/isolation & purification , Plants, Medicinal/chemistry , Plants, Medicinal/enzymology , Plants, Medicinal/genetics , Protein Engineering/methods , Structure-Activity Relationship
14.
Methods Enzymol ; 656: 375-428, 2021.
Article in English | MEDLINE | ID: mdl-34325793

ABSTRACT

Over the past decade, harnessing the cellular protein synthesis machinery to incorporate non-canonical amino acids (ncAAs) into tailor-made peptides has significantly advanced many aspects of molecular science. More recently, groundbreaking progress in our ability to engineer this machinery for improved ncAA incorporation has led to significant enhancements of this powerful tool for biology and chemistry. By revealing the molecular basis for the poor or improved incorporation of ncAAs, mechanistic studies of ncAA incorporation by the protein synthesis machinery have tremendous potential for informing and directing such engineering efforts. In this chapter, we describe a set of complementary biochemical and single-molecule fluorescence assays that we have adapted for mechanistic studies of ncAA incorporation. Collectively, these assays provide data that can guide engineering of the protein synthesis machinery to expand the range of ncAAs that can be incorporated into peptides and increase the efficiency with which they can be incorporated, thereby enabling the full potential of ncAA mutagenesis technology to be realized.


Subject(s)
Amino Acids , Amino Acyl-tRNA Synthetases , Amino Acids/genetics , Amino Acyl-tRNA Synthetases/genetics , Mutagenesis , Protein Biosynthesis , Protein Engineering
15.
Future Med Chem ; 13(13): 1091-1103, 2021 07.
Article in English | MEDLINE | ID: mdl-34080888

ABSTRACT

Aim: This study investigated our Enzymelinks, COX-2-10aa-mPGES-1 and COX-2-10aa-PGIS, as cellular cross-screening targets for quick identification of lead compounds to inhibit inflammatory PGE2 biosynthesis while maintaining prostacyclin synthesis. Methods: We integrated virtual and wet cross-screening using Enzymelinks to rapidly identify lead compounds from a large compound library. Results: From 380,000 compounds virtually cross-screened with the Enzymelinks, 1576 compounds were identified and used for wet cross-screening using HEK293 cells that overexpressed individual Enzymelinks as targets. The top 15 lead compounds that inhibited mPGES-1 activity were identified. The top compound that specifically inhibited inflammatory PGE2 biosynthesis alone without affecting COX-2 coupled to PGI2 synthase (PGIS) for PGI2 biosynthesis was obtained. Conclusion: Enzymelink technology could advance cyclooxygenase pathway-targeted drug discovery to a significant degree.


Subject(s)
Benzene Derivatives/pharmacology , Cyclooxygenase 1/metabolism , Cytochrome P-450 Enzyme System/metabolism , Intramolecular Oxidoreductases/metabolism , Protein Engineering , Benzene Derivatives/chemistry , Drug Evaluation, Preclinical , HEK293 Cells , Humans , Microsomes/drug effects , Microsomes/enzymology
16.
Cell ; 184(10): 2779-2792.e18, 2021 05 13.
Article in English | MEDLINE | ID: mdl-33915107

ABSTRACT

Ligands can induce G protein-coupled receptors (GPCRs) to adopt a myriad of conformations, many of which play critical roles in determining the activation of specific signaling cascades associated with distinct functional and behavioral consequences. For example, the 5-hydroxytryptamine 2A receptor (5-HT2AR) is the target of classic hallucinogens, atypical antipsychotics, and psychoplastogens. However, currently available methods are inadequate for directly assessing 5-HT2AR conformation both in vitro and in vivo. Here, we developed psychLight, a genetically encoded fluorescent sensor based on the 5-HT2AR structure. PsychLight detects behaviorally relevant serotonin release and correctly predicts the hallucinogenic behavioral effects of structurally similar 5-HT2AR ligands. We further used psychLight to identify a non-hallucinogenic psychedelic analog, which produced rapid-onset and long-lasting antidepressant-like effects after a single administration. The advent of psychLight will enable in vivo detection of serotonin dynamics, early identification of designer drugs of abuse, and the development of 5-HT2AR-dependent non-hallucinogenic therapeutics.


Subject(s)
Biosensing Techniques , Designer Drugs/chemistry , Designer Drugs/pharmacology , Drug Discovery/methods , Hallucinogens/chemistry , Hallucinogens/pharmacology , Receptor, Serotonin, 5-HT2A/chemistry , Animals , Drug Evaluation, Preclinical/methods , Female , Fluorescence , Fluorescent Dyes/chemistry , HEK293 Cells , Humans , Male , Mice , Mice, Inbred C57BL , Photometry , Protein Conformation , Protein Engineering , Receptor, Serotonin, 5-HT2A/genetics , Receptor, Serotonin, 5-HT2A/metabolism , Serotonin/metabolism , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology
17.
Int J Mol Sci ; 22(7)2021 Mar 27.
Article in English | MEDLINE | ID: mdl-33801752

ABSTRACT

Bovine mastitis is a significant economic burden for dairy enterprises, responsible for premature culling, prophylactic and therapeutic antibiotic use, reduced milk production and the withholding (and thus wastage) of milk. There is a desire to identify novel antimicrobials that are expressly directed to veterinary applications, do not require a lengthy milk withholding period and that will not have a negative impact on the growth of lactic acid bacteria involved in downstream dairy fermentations. Nisin is the prototypical lantibiotic, a family of highly modified antimicrobial peptides that exhibit potent antimicrobial activity against many Gram-positive microbes, including human and animal pathogens including species of Staphylococcus and Streptococcus. Although not yet utilized in the area of human medicine, nisin is currently applied as the active agent in products designed to prevent bovine mastitis. Over the last decade, we have harnessed bioengineering strategies to boost the specific activity and target spectrum of nisin against several problematic microorganisms. Here, we screen a large bank of engineered nisin derivatives to identify novel derivatives that exhibit improved specific activity against a selection of staphylococci, including mastitis-associated strains, but have unchanged or reduced activity against dairy lactococci. Three such peptides were identified; nisin A M17Q, nisin A T2L and nisin A HTK.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bacteriocins/pharmacology , Lactococcus/drug effects , Mastitis, Bovine/microbiology , Nisin/chemistry , Staphylococcus/drug effects , Animals , Bioengineering/methods , Cattle , Female , Microbial Sensitivity Tests , Milk/microbiology , Peptides/chemistry , Protein Engineering/methods
18.
Plant Cell Rep ; 40(4): 723-733, 2021 Apr.
Article in English | MEDLINE | ID: mdl-33582859

ABSTRACT

KEY MESSAGE: Plant expression platform is the new source of immunoglobulin G (IgG) toward small low-molecular-weight targets. The plant-made monoclonal antibody-based immunoassay exhibits comparable analytical performance with hybridoma antibody. Immunoassays for small molecules are efficiently applied for monitoring of serum therapeutic drug concentration, food toxins, environmental contamination, etc. Immunoglobulin G (IgG) is usually produced using hybridoma cells, which requires complicated procedures and expensive equipment. Plants can act as alternative and economic hosts for IgG production. However, the production of free hapten (low-molecular-weight target)-recognizing IgG from plants has not been successfully developed yet. The current study aimed at creating a plant platform as an affordable source of IgG for use in immunoassays and diagnostic tools. The functional IgG was expressed in Nicotiana benthamiana leaves infiltrated with Agrobacterium tumefaciens strain GV3101 with recombinant geminiviral vectors (pBY3R) occupying chimeric anti-miroestrol IgG genes. The appropriate assembly between heavy and light chains was achieved, and the yield of expression was 0.57 µg/g fresh N. benthamiana leaves. The binding characteristics of the IgG to miroestrol and binding specificity to related compounds, such as isomiroestrol and deoxymiroestrol, were similar to those of hybridoma-produced IgG (monoclonal antibody, mAb). The plant-based mAbs exhibited high sensitivity for miroestrol (IC50, 23.2 ± 2.1 ng/mL), precision (relative standard deviation ≤ 5.01%), and accuracy (97.8-103% recovery), as determined using quantitative enzyme-linked immunosorbent assay. The validated enzyme-linked immunosorbent assay was applicable to determine miroestrol in plant samples. Overall, the plant-produced functional IgG conserved the binding activity and specificity of the parent IgG derived from mammalian cells. Therefore, the plant expression system may be an efficient and affordable platform for the production of antibodies against low-molecular-weight targets in immunoassays.


Subject(s)
Immunoassay/methods , Immunoglobulin G/genetics , Nicotiana/genetics , Protein Engineering/methods , Steroids/immunology , Antibodies, Monoclonal/genetics , Antibodies, Monoclonal/immunology , Antibodies, Monoclonal/isolation & purification , Cross Reactions , Enzyme-Linked Immunosorbent Assay/methods , Immunoglobulin G/immunology , Plant Extracts/analysis , Plants, Genetically Modified , Pueraria/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/immunology , Steroids/analysis
19.
Int J Pharm ; 596: 120265, 2021 Mar 01.
Article in English | MEDLINE | ID: mdl-33486031

ABSTRACT

Rising cases of Non melanoma skin carcinoma (NMSC) and escalating levels of ultraviolet radiations have underlined a profound correlation with the elevating levels of environmental detoriation and increasing health issues. However, the availability of therapeutics has not aided in controlling the recurrence rates of skin carcinoma. Frequent administration of therapeutics with higher chances of facial deformity escalates the patient's treatment expenses. Thus, this study initiates a low cost effective and biodegradable therapy by exploring four formulations with combinations of silver nanoparticles (AgNPs), sericin (isolated from cocoons of Antherea mylitta) and chitosan. Subsequently, various ethosomal formulations were evaluated as a platform for transdermal delivery vehicle for efficient skin intervention therapeutics. Characterization using UV visible spectroscopy, Dynamic light scattering, Fourier Infrared spectroscopy, X-ray dispersion, Transmission electron microscopy, Fluorescence assisted cell sorting and in vitro studies were done and it was inferenced that equal combination of AgNPs and sericin facilitated to combat the morphological and cellular deformation of the epidermoid A431skin carcinoma cells. The overproduction of superoxide (O2.) and nitric oxide (NO) radicals consequently depolarized the mitochondrial membrane potential triggering apoptosis and necrosis. The in vivo experiments exhibited the stimulation of IgM secretion with T cell-mediated immune response. Therefore, this study proposes a novel approach for treatment of NMSC using biocompatible formulations delivered through ethosomes.


Subject(s)
Carcinoma , Chitosan , Metal Nanoparticles , Sericins , Humans , Protein Engineering , Silver
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