Biocatalysis: landmark discoveries and applications in chemical synthesis

Biocatalysis has become an important tool in chemical synthesis, allowing access to complex molecules with high levels of activity and selectivity and with low environmental impact. Key discoveries in protein engineering, bioinformatics, recombinant technology and DNA sequencing have contributed towards the rapid acceleration of the field. This tutorial review explores enzyme engineering strategies and high-throughput screening approaches that have been applied for the discovery and development of enzymes for synthetic application. Landmark developments in the field are discussed and have been carefully selected to highlight the diverse synthetic applications of enzymes within the pharmaceutical, agricultural, food and chemical industries. The design and development of artificial biocatalytic cascades is also examined. This tutorial review will give readers an insight into the landmark discoveries and milestones that have helped shape and grow this branch of catalysis since the discovery of the first enzyme.

Strategies for designing biocatalysts with new functions

The engineering of natural enzymes has led to the availability of a broad range of biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and pharmaceuticals. However, for many important chemical transformations there are no known enzymes that can serve as starting templates for biocatalyst development. These limitations have fuelled efforts to build entirely new catalytic sites into proteins in order to generate enzymes with functions beyond those found in Nature. This bottom-up approach to enzyme development can also reveal new fundamental insights into the molecular origins of efficient protein catalysis. In this tutorial review, we will survey the different strategies that have been explored for designing new protein catalysts. These methods will be illustrated through key selected examples, which demonstrate how highly proficient and selective biocatalysts can be developed through experimental protein engineering and/or computational design. Given the rapid pace of development in the field, we are optimistic that designer enzymes will begin to play an increasingly prominent role as industrial biocatalysts in the coming years.

Multicomponent Synthesis of the SARS-CoV-2 Main Protease Inhibitor Nirmatrelvir

In the wake of the Covid-19 pandemic, it has become clear that global access to efficacious antiviral drugs will be critical to combat future outbreaks of SARS-CoV-2 or related viruses. The orally available SARS-CoV-2 main protease inhibitor nirmatrelvir has proven an effective treatment option for Covid-19, especially in compromised patients. We report a new synthesis of nirmatrelvir featuring a highly enantioselective biocatalytic desymmetrization (>99% ee) and a highly diastereoselective multicomponent reaction (>25:1 dr) as the key steps. Our route avoids the use of transition metals and peptide coupling reagents, resulting in an overall highly efficient and atom-economic process.

Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of functional histidine analogues

The availability of an expanded genetic code opens exciting new opportunities in enzyme design and engineering. In this regard histidine analogues have proven particularly versatile, serving as ligands to augment metalloenzyme function and as catalytic nucleophiles in designed enzymes. The ability to genetically encode multiple functional residues could greatly expand the range of chemistry accessible within enzyme active sites. Here, we develop mutually orthogonal translation components to selectively encode two structurally similar histidine analogues. Transplanting known mutations from a promiscuous Methanosarcina mazei pyrrolysyl-tRNA synthetase (MmPylRSIFGFF ) into a single domain PylRS from Methanomethylophilus alvus (MaPylRSIFGFF ) provided a variant with improved efficiency and specificity for 3-methyl-L-histidine (MeHis) incorporation. The MaPylRSIFGFF clone was further characterized using in vitro biochemical assays and x-ray crystallography. We subsequently engineered the orthogonal MmPylRS for activity and selectivity for 3-(3-pyridyl)-L-alanine (3-Pyr), which was used in combination with MaPylRSIFGFF to produce proteins containing both 3-Pyr and MeHis. Given the versatile roles played by histidine in enzyme mechanisms, we anticipate that the tools developed within this study will underpin the development of enzymes with new and enhanced functions.

Design and evolution of an enzyme with a non-canonical organocatalytic mechanism

The combination of computational design and laboratory evolution is a powerful and potentially versatile strategy for the development of enzymes with new functions^1-4. However, the limited functionality presented by the genetic code restricts the range of catalytic mechanisms that are accessible in designed active sites. Inspired by mechanistic strategies from small-molecule organocatalysis⁵, here we report the generation of a hydrolytic enzyme that uses N_δ-methylhistidine as a non-canonical catalytic nucleophile. Histidine methylation is essential for catalytic function because it prevents the formation of unreactive acyl-enzyme intermediates, which has been a long-standing challenge when using canonical nucleophiles in enzyme design^6-10. Enzyme performance was optimized using directed evolution protocols adapted to an expanded genetic code, affording a biocatalyst capable of accelerating ester hydrolysis with greater than 9,000-fold increased efficiency over free N_δ-methylhistidine in solution. Crystallographic snapshots along the evolutionary trajectory highlight the catalytic devices that are responsible for this increase in efficiency. N_δ-methylhistidine can be considered to be a genetically encodable surrogate of the widely employed nucleophilic catalyst dimethylaminopyridine¹¹, and its use will create opportunities to design and engineer enzymes for a wealth of valuable chemical transformations.

3-Hydroxypyrrolidine and (3,4)-dihydroxypyrrolidine derivatives: inhibition of rat intestinal α-glucosidase

Thirteen pyrrolidine-based iminosugar derivatives have been synthesized and evaluated for inhibition of α-glucosidase from rat intestine. The compounds studied were the non-hydroxy, mono-hydroxy and dihydroxypyrrolidines. All the compounds were N-benzylated apart from one. Four of the compounds had a carbonyl group in the 2,5-position of the pyrrolidine ring. The most promising iminosugar was the trans-3,4-dihydroxypyrrolidine 5 giving an IC50 of 2.97±0.046 and a KI of 1.18 mM. Kinetic studies showed that the inhibition was of the mixed type, but predominantly competitive for all the compounds tested. Toxicological assay results showed that the compounds have low toxicity. Docking studies showed that all the compounds occupy the same region as the DNJ inhibitor on the enzyme binding site with the most active compounds establishing similar interactions with key residues. Our studies suggest that a rotation of ∼90° of some compounds inside the binding pocket is responsible for the complete loss of inhibitory activity. Despite the fact that activity was found only in the mM range, these compounds have served as simple molecular tools for probing the structural features of the enzyme, so that inhibition can be improved in further studies.

Incidence of pulmonary edema after tracheotomy for obstructive sleep apnea

OBJECTIVE

The phenomenon of postobstructive pulmonary edema (POPE) has been associated with the relief of upper airway obstruction, which itself is fundamental to the pathophysiology of obstructive sleep apnea (OSA). A review of patients with OSA undergoing tracheotomy was performed to characterize this process.

STUDY DESIGN

Retrospective chart review of study patients with OSA undergoing tracheotomy and of control patients without OSA undergoing tracheotomy for unrelated problems. Chest radiographs were reviewed in a double-blind fashion to score posttracheotomy changes in pulmonary status.

SETTING

Academic tertiary referral center.

RESULTS

Thirty (67%) of 45 OSA patients treated by tracheotomy had evidence of POPE, whereas only 5 (20%) of 25 control group patients had increased pulmonary edema. The remaining 15 (33%) of 45 OSA patients and 20 (80%) of 25 control patients had either no change or an improved pulmonary status. Those with OSA that developed POPE were mostly graded as having mild pulmonary edema (22/30, 73%). Far fewer were graded as having moderate pulmonary edema (6/30, 20%), and fewer still with severe pulmonary edema (2/30, 7%). Two (7%) of 45 patients with severe POPE died of complications related to cor pulmonale in the postoperative period.

CONCLUSION

Results support maintaining a high index of suspicion for the development of postobstructive pulmonary edema in patients treated for OSA. Treatment options, such as positive pressure ventilation and diuresis, and an increased awareness of this condition may help reduce the morbidity and mortality associated with treatment of this disease.

Evaluation of airway obstruction using virtual endoscopy

OBJECTIVES

This study examines the use of virtual endoscopy (VE) in the evaluation of patients with upper airway obstruction. The utility of VE compared with actual endoscopy was investigated with respect to accuracy of diagnosis and reproduction of endoscopic images.

STUDY DESIGN

A random cohort of 30 patients with various causes of airway obstruction was examined.

METHODS

The computed tomography (CT) data were reconstructed using a proprietary VE software program, FreeFlight, blind to the actual endoscopic findings. The cause of obstruction was identified and compared with actual endoscopic findings. This included 21 patients with airway stenoses, 8 patients with laryngotracheomalacia, 3 tracheal tumors, 2 glottic webs, 5 patients with innominate artery compression, 2 tracheal granulomas, and 7 patients with impaired true vocal cord mobility.

RESULTS

Virtual endoscopic evaluation was accurate in assessing stenosis width and length of fixed airway lesions. Correlation of stenosis shape and contour between actual endoscopy and VE was excellent. The stenosis-to-lumen ratios were compared between VE and actual endoscopy and were found to be within 10% (SD = 8). However, virtual endoscopic evaluation could not illustrate one of the glottic webs, half of the cases of tracheomalacia, or any of the cases of impaired true vocal cord mobility.

CONCLUSIONS

Virtual endoscopy was not as sensitive as actual endoscopy in detecting the cause of airway obstruction that was based on dynamic movement. However, VE was excellent for the measurement and definition of fixed airway lesions.

Benefits of routine maxillectomy and orbital reconstruction with the rectus abdominis free flap

Maxillary defects lead to functional and cosmetic deficiencies, especially with tumor invasion of the orbit and cribriform plate. Additionally problematic is the near-total palatal resection in patients with poor dentition (ie, not useful for anchoring obturators) and the desire for return of deglutition and useful speech. A series of 12 patients is presented in whom a rectus abdominis free flap was used for reconstruction of the palate, maxilla, and/or orbit. Nine of 12 free flaps were used to reconstruct defects involving the maxilla and orbit; all were successful in restoring hard palate continuity and function without the use of an obturator. The remaining 3 patients underwent successful repair of defects involving the orbit and medial maxilla without complication. Four of those 9 patients with palatal reconstruction augmented their dental rehabilitation with either their existing upper denture plate or the use of a cosmetic appliance anchored to their remaining dentition. Objectively, the rectus abdominis myocutaneous free flap proved to be a reliable and expeditious method of restoring function and acceptable cosmesis. We believe this technique should be routinely considered in the reconstruction of these defects.

The etiology and pathogenesis of laryngeal carcinoma

Epidemiologic data suggest that the etiology and pathogenesis of laryngeal carcinoma are influenced by environmental and lifestyle-related factors, such as tobacco use, ethanol consumption, and exposure to toxic substances. In addition, dietary factors, irradiation, papilloma virus infection, and laryngopharyngeal reflux seem to be significant carcinogenic cofactors. This article presents a multi-factorial model of laryngeal mucosal carcinogenesis.

The role of epidural cortisone injection in the treatment of diskogenic low back pain

Primary treatment by epidural injection of cortisone in patients suffering from characteristic diskogenic disease was helpful in 82% of patients. However, when given after three months of back pain, after previous laminectomies, and in patients actually suffering from an unstable spine which required fusion, epidural injections were of little value. No complications resulted from the injection and there was no compelling evidence to indicate that the placement of the needle by radiologic means is necessary. Because of these benefits and the fact that all of the patients were candidates for laminectomy, the use of this injection prior to surgery should be considered. The number of injections that may reasonably be given, the degree to which the patient should become asymptomatic, and the period of time during which relief continues remain to be clarified by a larger and more sustained study.