Biofuel–Pharmaceutical Co-Production in Integrated Biorefineries: Strategies, Challenges, and Sustainability

Abstract

Global demands for sustainable energy and advanced therapeutics necessitate innovative interdisciplinary solutions. Integrated biorefining emerges as a strategic response, enabling the co-production of biofuels and pharmaceutical compounds through biomass valorization. This integrated model holds promise in enhancing resource utilization efficiency while ensuring economic viability. Our critical review methodically evaluates seven pivotal methodologies: seven key strategies: microbial metabolites, synthetic biology platforms, biorefinery waste extraction, nanocatalysts, computer-aided design, extremophiles, and plant secondary metabolites. Through systematic integration of these approaches, we reveal pivotal synergies and potential technological innovations that can propel multi-product biorefinery systems. Persistent challenges, particularly in reconciling complex metabolic flux balancing with regulatory compliance requirements, are analyzed. Nevertheless, advancements in systems biology, next-generation bioprocess engineering, and artificial intelligence-enhanced computational modeling present viable pathways for overcoming these obstacles. This comprehensive analysis substantiates the transformative capacity of integrated biorefining in establishing a circular bioeconomy framework, while underscoring the imperative of transdisciplinary cooperation to address existing technical and policy constraints.

1. Introduction

The 21st century faces two major global challenges: shifting to sustainable energy systems to address climate change and ensure energy security and continually searching for new and effective medicines to fight human diseases [1,2]. Although traditionally separate fields, energy production and pharmaceutical development are increasingly coming together, driven by advances in biotechnology and integrated biorefining [3,4,5]. The biorefinery concept, which involves processing biomass into a range of products like fuels, chemicals, and materials, provides a foundation for this synergy [6,7,8]. Strategically producing high-volume, lower value biofuels together with low-volume, high-value pharmaceuticals or their precursors and using shared feedstocks and infrastructure can significantly enhance the overall economic viability and sustainability of bio-based production [9,10,11]. Central to this integrated approach are microorganisms and plants; their vast metabolic diversity and suitability for engineering make them versatile biological factories [12,13].

With increasing interest in biorefineries and bio-based product manufacturing, there is an urgent need to systematically review advances in the integrated co-production of biofuels and pharmaceuticals. Furthermore, biorefineries can simultaneously produce other high-value substances (such as biochemicals including C1 compounds like carbon monoxide and hydrogen, C2 compounds such as ethanol, C3 compounds like glycerol and lactic acid, C4 compounds such as succinic acid, C5 derivatives like levulinic acid, and C6 derivatives such as 5-hydroxymethylfurfural and 2,5-furandicarboxylic acid), bioplastics (e.g., starch-based or lignin-based polymers), as well as proteins and fertilizers [14]. This review addresses that gap by providing a comprehensive overview of the strategies and technologies that enable the simultaneous production of these two valuable product streams within the same biorefinery framework. We examine a range of approaches, including the utilization of diverse microbial metabolites, the application of synthetic biology for targeted production, the valorization of biorefinery waste streams, the role of advanced nanocatalysts, the potential of extremophiles, and the integrated use of plant secondary metabolites (Figure 1). Additionally, we identify key challenges that must be overcome to make co-production economically and technically viable, such as optimizing metabolic pathways, developing efficient separation techniques, and scaling up processes. Furthermore, we clearly identify and discuss the overarching technical, economic, and regulatory challenges inherent in this interdisciplinary field, concluding with an outlook on future prospects and necessary advancements to fully realize its potential.

To ensure a comprehensive review, we conducted a systematic search across multiple databases, including PubMed, Scopus, Web of Science, and Google Scholar, to capture a wide range of relevant scientific literature. The search was performed using a combination of keywords such as biofuel, pharmaceutical, biorefinery, synthetic biology, metabolic engineering, nanocatalysts, extremophiles, and specific terms related to pharmaceutical compounds. The time range spanned from January 2010 to April 2025, with a particular emphasis on studies published between 2020 and 2025 to prioritize the most recent advancements in the field. Inclusion criteria were applied to select studies that addressed the integration of biofuel and pharmaceutical production within biorefineries or cross-disciplinary reference value, while exclusion criteria eliminated studies focusing solely on either biofuel or pharmaceutical production without their integration or capability. This review intentionally adopts a macro-level synthesis focusing on strategy interoperability and conceptual innovation rather than replicating process details already documented in references.

2. Dual-Purpose Development of Microbial Metabolites

Utilizing microbial metabolites provides a synergistic approach to achieving biofuel–pharmaceutical co-production. Microorganisms such as algae, bacteria, yeasts, and fungi possess diverse metabolic capabilities, enabling them to convert various feedstocks into biofuels like ethanol, butanol, lipids for biodiesel, or hydrogen, as well as high-value pharmaceutical compounds including antioxidants, anticancer agents, anti-inflammatory substances, pigments, and essential fatty acids [15]. This integrated strategy, often within biorefineries, aims to improve economic viability and sustainability. It does this by better utilizing biomass, sharing resources between production processes, possibly lowering separation and purification costs, and adding value to all major products from the microbial biomass [16]. Key microbial examples and their dual-output capabilities are systematically summarized in

Table 1. Examples of microbial metabolites for dual biofuel and pharmaceutical production.

Microorganism	Biofuel(s)/Precursors	Pharmaceuticals/Precursors	Refs.
Acinetobacter spp.	Biodiesel	Potential for emulsifiers/biosurfactants—varies by species	[17,18]
Bacillus spp.	Biodiesel	Bioacetoin	[19,20]
Chlamydomonas reinhardtii	Hydrogen, Biodiesel	Carotenoids (β-carotene, astaxanthin)	[21,22,23]
Clostridium acetobutylicum	Butanol	Butyric Acid	[24,25]
Dunaliella salina	Biodiesel	β-carotene (antioxidant, vitamin A precursor)	[26,27,28]
Haematococcus pluvialis	Biodiesel, Ethanol, Biogas (from residual biomass)	Astaxanthin (antioxidant, anti-inflammatory, neuroprotective)	[29,30,31]
Mortierella isabellina	Biodiesel	Gamma-linolenic acid (anti-inflammatory)	[32,33,34]
Phaffia rhodozyma	Biodiesel (from lipids)	Astaxanthin (antioxidant, anti-inflammatory, neuroprotective)	[35,36]
Phormidium sp.	Biodiesel	Squalene	[37,38]
Rhizopus oryzae	Biodiesel	Chitin/Chitosan (biomedical polymers)	[39,40,41]
Rhodotorula babjevae Y-SL7	Microbial oil (>40%)	Polyol Esters of Fatty Acids	[42,43]
Rhodotorula glutinis	Biodiesel	Carotenoids (β-carotene, torulene, torularhodin-antioxidants)	[44,45]
Rhodotorula kratochvilovae SY89	Biodiesel	Carotenoids, β-glucans (immunostimulatory), Exoglycolipids	[46,47,48]
Rhodococcus spp.	Biodiesel	Potential for steroid biotransformation—varies by species	[49,50,51]
Spirulina (Arthrospira platensis)	Biodiesel	Phycocyanin (antioxidant, anti-inflammatory)	[52,53]
Yarrowia lipolytica	Biodiesel	Omega-3 fatty acids, Carotenoids, Flavonoids (engineered, e.g., naringenin), Lipases	[54,55,56,57,58,59]

.

Selecting suitable microorganisms primarily hinges on the desired end products, the type of feedstock available—ranging from simple sugars to complex lignocellulosic materials or even CO₂—and their compatibility with downstream processing requirements for both fuel and pharmaceutical-grade outputs. The microalga Haematococcus pluvialis is one of the most studied examples. This microorganism is renowned for accumulating astaxanthin, a potent antioxidant, at high concentrations—reaching up to 5% of its dry weight under stress conditions [30]. This carotenoid is widely used in nutraceuticals and studied for pharmaceutical uses because of its anti-inflammatory and neuroprotective properties. The residual algal biomass left after astaxanthin extraction contains valuable lipids and carbohydrates, making it an ideal feedstock for biodiesel production through transesterification, bioethanol via fermentation, or biogas through anaerobic digestion. This shows a clear path for sequential co-production [60]. Clostridium acetobutylicum is a key bacterium in the traditional Acetone-Butanol-Ethanol fermentation. It mainly produces butanol, a promising advanced biofuel [25]. However, its metabolism also produces butyric acid, an intermediate attracting interest for its potential anticancer properties, especially when used in targeted prodrugs like pivaloyloxymethyl butyrate [61,62]. The oleaginous yeast Phaffia rhodozyma naturally synthesizes astaxanthin while also accumulating significant quantities of lipids, particularly triglycerides, making it suitable for concurrent production of this valuable pigment and biodiesel precursors [63]. Similarly, other yeasts belonging to the Rhodotorula genus, such as Rhodotorula glutinis, are known co-producers, yielding lipids suitable for biodiesel alongside various carotenoids including β-carotene, torulene, and torularhodin, which function as antioxidants and potential provitamin A sources [64]. Specific strains like Rhodotorula babjevae Y-SL7 demonstrate remarkable capability on crude glycerol—a biodiesel byproduct, accumulating over 40% lipids while secreting potentially valuable polyol esters of fatty acids. Rhodotorula kratochvilovae SY89 further demonstrates this metabolic diversity through simultaneous production of lipids with yields reaching 66.7% of its biomass, along with carotenoids, immunostimulatory cell wall β-glucans, and extracellular glycolipids. [64,65]. The cyanobacterium Spirulina (genus Arthrospira, e.g., A. platensis), cultivated globally as a food supplement, produces the blue pigment phycocyanin, valued for its antioxidant, anti-inflammatory, and potential anticancer properties, alongside lipids that can be utilized for biodiesel production, showcasing co-production in photosynthetic microbes [66,67]. Oleaginous fungi, like Mortierella isabellina, accumulate lipids often rich in valuable polyunsaturated fatty acids such as gamma-linolenic acid, used therapeutically for inflammatory conditions, while the bulk lipid fraction remains suitable for biodiesel conversion [32]. Model organisms like the green alga Chlamydomonas reinhardtii offer potential for producing hydrogen or lipids as biofuels [68], coupled with β-carotene and potentially astaxanthin under specific stress conditions [23]. The extremophilic alga Dunaliella salina, which thrives in hypersaline environments, is commercially valued not only for its remarkably high β-carotene content reaching up to 14% of dry weight but also for accumulating lipids suitable for biodiesel production [26]. The versatile oleaginous yeast Yarrowia lipolytica has become a workhorse in metabolic engineering, capable of high lipid accumulation from various substrates and engineered to produce diverse compounds including omega-3 fatty acids, carotenoids, and even non-native products like flavonoids through synthetic biology approaches [69,70]. Bacterial systems, including species of Rhodococcus, and others like Bacillus, and Acinetobacter, known for lipid accumulation, can also be engineered or utilized for producing precursors like bioacetoin [71]. Other documented examples include the cyanobacterium Phormidium sp., which generates both lipids and squalene—a high value precursor for cosmetic and pharmaceutical applications [72,73], and the fungus Rhizopus oryzae generating lipids alongside chitin/chitosan polymers with biomedical applications [74].

The wide metabolic diversity found in various microbial groups—including algae, yeasts, bacteria, fungi, and archaea—provides many opportunities for the integrated production of biofuels and valuable pharmaceutical or nutraceutical compounds [75]. Further exploration of microbial diversity [76], combined with progress in metabolic engineering, synthetic biology [77], systems biology tools, and the development of efficient, integrated bioprocessing methods [78], is essential. These advances are needed to overcome current challenges and realize the full industrial potential of these dual-purpose microbial systems for making both energy and health products at the same time.

3. Dual Applications of Synthetic Biology Platforms

Synthetic biology offers a powerful engineering framework. It uses standardized genetic parts, quantitative modeling, and rational design principles to build and optimize biological systems for new purposes, including the customized co-production of biofuels and pharmaceuticals [79]. Furthermore, integrating high-throughput screening methods, biosensors for monitoring pathways dynamically, and advanced gene editing tools like CRISPR-Cas9 significantly speeds up the design–build–test–learn cycle, facilitating rapid optimization of these dual-production systems [77,80,81].

Table 2. Examples of synthetic biology platforms for dual applications.

Engineered Organism	Synthetic Biology Approach	Biofuel(s)/Precursors	Pharmaceuticals	Refs.
Escherichia coli	Pathway engineering, Gene expression optimization, Metabolic flux control	Fatty acid ethyl esters, Alkanes, Isoprenoid fuels	Lycopene, Amorphadiene (artemisinin precursor), Other isoprenoids	[82,83,84,85,86,87,88]
Microbial Consortia	Division of labor, Cross-feeding between engineered strains	Varies (e.g., H2 + CO2 -> methane/acetate)	Varies (e.g., sequential biotransformation for complex drugs)	[89,90,91,92]
Saccharomyces cerevisiae	Metabolic engineering, Heterologous pathway construction, CRISPR-Cas9	Ethanol, Isobutanol, Farnesene, Other alcohols	Artemisinic acid (artemisinin precursor), Resveratrol, Insulin precursors, Polyketides	[93,94,95,96,97,98,99]
Synechocystis sp. PCC 6803 (Cyanobacterium)	Photosynthetic pathway engineering, CO2 fixation enhancement, CRISPR-Cas9	Isobutanol, Ethanol, Fatty acids, Limonene	β-carotene, Phycocyanin, Terpenoid precursors, Other bioactive compounds	[100,101,102,103,104,105]
Various (using advanced tools)	Biosensors, Dynamic regulatory circuits, High-throughput screening	Optimized yield/titer	Optimized yield/titer, Balanced co-production	[106,107,108]
Yarrowia lipolytica	Metabolic engineering, Lipid pathway optimization, CRISPR-Cas9, Pathway compartmentalization	Biodiesel	Omega-3 fatty acids (EPA, DHA), Carotenoids, Polyketides	[59,109,110,111,112,113,114,115]

summarizes representative examples of synthetic biology platforms for dual applications.

The practical application of synthetic biology in developing dual-purpose platforms is demonstrated through numerous successful examples across various microbial hosts [79]. Strains have been engineered to produce biofuels such as fatty acid ethyl esters or short-chain alkanes by introducing relevant biosynthetic pathways, while simultaneously optimizing native pathways or incorporating heterologous modules for the synthesis of valuable isoprenoids like lycopene or amorphadiene, the sesquiterpene precursor to the crucial antimalarial drug artemisinin [116]. Similarly, Saccharomyces cerevisiae, favored for its robustness in industrial fermentations, has been a prime target for synthetic biology approaches [117]. Seminal work led to yeast strains capable of producing high titers of artemisinic acid through the complex multi-gene engineering of the mevalonate pathway and introduction of amorphadiene synthase and P450 monooxygenase enzymes; this artemisinic acid is then chemically converted to artemisinin [116]. These same engineered yeast platforms, or parallel strains, can be optimized for the production of biofuels like ethanol, isobutanol, or the jet fuel precursor farnesene, often utilizing lignocellulosic hydrolysates as feedstock [117]. Other notable yeast engineering achievements include simultaneous production of ethanol with resveratrol, a high-value antioxidant linked to red wine, or with precursors to human insulin [118]. Photosynthetic microorganisms, such as cyanobacteria like Synechocystis sp. PCC 6803, offer the unique advantage of utilizing atmospheric CO₂ as a carbon source [119]. Synthetic biology tools have been employed to redirect carbon fixed through photosynthesis towards biofuels like isobutanol, ethanol, or fatty acids, while also enhancing the production of native pigments with pharmaceutical potential including β-carotene and phycocyanin, or introducing pathways for novel pharmaceutical precursors [119]. The non-conventional oleaginous yeast Yarrowia lipolytica is another rapidly emerging platform, amenable to synthetic biology manipulations for the hyper-accumulation of lipids alongside engineered production of high-value molecules like omega-3 fatty acids or carotenoids [120].

Continued advances in synthetic biology tools, combined with deeper systems-level understanding and effective process integration, will be crucial for realizing the commercial potential of these dual-purpose platforms and establishing them as impactful industrial applications.

4. Extraction of Medicinal Components from Biorefinery Waste

The transition towards a circular bioeconomy necessitates maximizing value creation from biomass resources. Biorefineries, designed to convert biomass into fuels and chemicals, typically generate substantial amounts of side streams. Examples include lignin from lignocellulosic processing, spent microbial biomass after fermentation or extraction, and residual liquids such as hemicellulose hydrolysates or fermentation broth. These streams are often considered low-value waste or used for basic applications like animal feed or energy generation through combustion. Yet, they frequently hold a rich source of untapped bioactive components with potential uses in medicine, nutraceuticals, or cosmetics [121], as summarized in

Table 3. Examples of medicinal components extracted from biorefinery waste.

Biorefinery Waste Stream	Extracted Medicinal Component(s)	Potential Medicinal Application(s)	Refs.
Crude Glycerol from Biodiesel	Impurities potentially convertible, e.g., to 1,3-propanediol	Chemical intermediate	[122,123,124]
Fermentation Residues	Residual enzymes, Bioactive Peptides, Phenolic compounds, Microbial biomass components	Antimicrobial, Antioxidant, Enzyme source, Animal feed supplement	[125,126,127,128,129]
Fungal Biomass Residues	Chitin, Chitosan	Drug delivery, Wound healing, Tissue engineering	[130,131,132,133,134,135]
Hemicellulose Hydrolysate	Phenolic acids, Oligosaccharides	Antioxidant, Prebiotic	[136,137,138,139]
Lignocellulosic Residues	Phenolic monomers/oligomers	Antioxidant, Antimicrobial, Anti-inflammatory, Flavorant, Chemical precursor	[140,141,142,143,144,145,146,147]
Spent Microalgal Biomass (post-primary extraction)	Bioactive Peptides, Proteins, β-glucans, Residual Carotenoids, Chlorophyll derivatives, Omega-3 fatty acids, Minerals	Antioxidant, Antihypertensive, Immunostimulatory, Antimicrobial, Nutritional supplement	[145,148,149,150,151,152]

which catalogs representative medicinal components extractable from major biorefinery side streams alongside their applications.

Lignocellulosic biorefineries process feedstocks including wood, agricultural residues such as straw and stover, or energy grasses, generating lignin as a major recalcitrant byproduct that typically accounts for 15–30% of the biomass. The complex polyphenolic structure of lignin renders it a promising source of valuable aromatic chemicals through depolymerization. Researchers employ diverse chemical methods like oxidation and hydrogenolysis, along with biological approaches including enzymatic treatment, to degrade lignin into lower molecular weight phenolic compounds. These breakdown products encompass vanillin, which serves as both flavorant and antioxidant; syringaldehyde; ferulic acid functioning as antioxidant and precursor; and p-coumaric acid with its antioxidant and anti-inflammatory properties—all finding established or emerging applications in pharmaceutical and food industries [153]. Hemicellulose hydrolysates, another stream from lignocellulosic pretreatment, primarily contain C5 and C6 sugars but also harbor minor yet potentially valuable components like phenolic acids (released from ester linkages) and oligosaccharides, particularly xylooligosaccharides derived from xylan. XOS are recognized for their prebiotic properties, promoting beneficial gut microbiota, and also exhibit antioxidant activity [154]. Microalgal biorefineries focused on lipid extraction for biodiesel leave behind substantial amounts of spent algal biomass. This protein-rich residue can be hydrolyzed to produce bioactive peptides with demonstrated antioxidant, antihypertensive (e.g., ACE-inhibitory), or antimicrobial activities [155]. Moreover, the residual biomass may retain valuable components including immunostimulatory β-glucans, various residual pigments such as carotenoids and chlorophyll derivatives, essential minerals, and residual omega-3 fatty acids, contingent upon the initial extraction efficiency [155]. Fermentation residues from bioethanol or ABE production, such as distiller’s dried grains with solubles from corn ethanol or the broth itself, are rich in microbial biomass, residual enzymes, proteins, and unfermented components including phenolic compounds derived from the original grain feedstock. These streams are potential sources for extracting enzymes, antimicrobial peptides, or antioxidant phytochemicals [156]. Similarly, biorefineries that process fungal biomass, particularly species such as Rhizopus oryzae used for lipid production, yield residues abundant in chitin and chitosan. These biocompatible polymers possess diverse biomedical applications owing to their hemostatic and antimicrobial properties, making them valuable for drug delivery systems, wound dressings, and tissue engineering scaffolds [157].

This “waste-to-value” strategy not only boosts profitability and diversifies product portfolios, but critically, it also supports resource circularity, minimizes environmental impact, and supplies sustainable sources of high-value compounds. This reinforces the argument that integrated biorefining is a cornerstone of the future bioeconomy.

5. Cross-Disciplinary Applications of Nanocatalysts

The convergence of nanotechnology and catalysis offers transformative potential for enhancing the efficiency, selectivity, and sustainability of chemical and biological processes central to integrated biofuel and pharmaceutical co-production [158]. In the biorefinery setting, nanocatalysts can be applied at various stages—from biomass pretreatment and fractionation to converting platform chemicals into advanced biofuels and synthesizing complex pharmaceutical intermediates [159]. This versatility makes them powerful cross-disciplinary tools for enabling new and efficient co-production pathways.

Table 4. Examples of cross-disciplinary applications of nanocatalysts.

Nanocatalyst Type	Process/Reaction Catalyzed	Relevance to Co-production	Refs.
Enzyme–Nanomaterial Conjugates	Transesterification; Esterification; Hydrolysis; Kinetic Resolution	Efficient biodiesel production; Synthesis/resolution of chiral drug precursors; Catalyst recovery and reuse via magnetic/physical separation.	[160,161,162,163,164]
Supported Metal NPs	Hydrogenation, Dehydrogenation, Oxidation, C-C Coupling, Hydrodeoxygenation	Upgrading biomass platform chemicals into fuel additives and pharmaceutical building blocks; Lignin depolymerization.	[165,166,167,168]
Metal Oxide Nanocatalysts	Photocatalysis; Oxidation; Acid/Base Catalysis	Biomass pretreatment enhancement; Biorefinery wastewater treatment; Specific organic synthesis for pharmaceuticals; Support material.	[169,170,171,172,173,174]
Bimetallic/Alloy Nanoparticles	Synergistic Catalysis	Enhanced activity/selectivity for hydrogenation, oxidation, C-C coupling in biomass upgrading, potentially benefiting both fuel/pharma pathways.	[175,176,177,178,179]
Nanocatalysts for Lignin Valorization	Selective Cleavage of Lignin Bonds	Controlled depolymerization of lignin waste into specific aromatic precursors for high-performance biofuels/materials and pharmaceuticals.	[180,181,182,183]
Multifunctional/Tandem Nanocatalysts	Cascade Reactions	One-pot conversion of biomass components or intermediates into advanced biofuels and pharmaceutical precursors, improving process efficiency.	[184,185,186,187,188]

summarizes representative nanocatalyst types along with their catalyzed processes and co-production relevance.

One prominent area is the development of nano-biocatalysts, where enzymes are immobilized onto nanostructured supports, often magnetic nanoparticles (MNPs), nanocellulose, graphene derivatives, or mesoporous silica. Lipases immobilized on MNPs demonstrate particularly high efficiency and reusability in biodiesel production through algal oil or waste cooking oil transesterification, where their performance is enhanced by convenient magnetic separation capabilities [189]. Importantly, these same immobilized lipases can be utilized for enantioselective reactions critical in pharmaceutical synthesis, such as the kinetic resolution of chiral alcohols or esters used as drug precursors [190]. Metal nanoparticles supported on high surface-area materials such as carbon nanotubes, metal oxides, and polymers represent another important category of extensively studied nanocatalysts. Supported palladium, platinum, ruthenium, or gold NPs exhibit high activity in hydrogenation, dehydrogenation, oxidation, and C-C coupling reactions. These reactions are crucial for upgrading biomass-derived platform chemicals, such as furfural and 5-hydroxymethylfurfural (HMF), obtained from C5 and C6 sugars [191]. Selective hydrogenation of furfural produces either furfuryl alcohol, which serves as a resin precursor, or tetrahydrofurfuryl alcohol, known as a green solvent. Further processing can convert these compounds into fuel additives such as valeric biofuels or C8-C12 alkanes. Simultaneously, these platform chemicals and their derivatives serve as versatile building blocks for synthesizing various pharmaceutical intermediates and fine chemicals [191]. Nanocatalysts are also playing a key role in lignin valorization. Specifically designed metal or metal oxide nanocatalysts are being developed to selectively cleave particular bonds such as β-O-4 ether linkages within the complex lignin polymer under relatively mild conditions. This targeted approach aims to generate well-defined aromatic monomers, primarily phenolics, which can function as valuable precursors. These monomers have dual applications, serving both as building blocks for high-performance polymer components potentially useful in advanced biofuels or materials and as sources for bioactive compounds including antioxidants and anti-inflammatory agents [192]. Photocatalytic nanomaterials, such as titanium dioxide and zinc oxide nanoparticles or nanocomposites, utilize light energy to drive redox reactions. Their applications in biorefineries include assisting biomass pretreatment, degrading recalcitrant organic pollutants in wastewater streams [193], and potentially enabling specific organic syntheses relevant to pharmaceuticals under ambient conditions. Moreover, researchers are developing multifunctional and tandem nanocatalysts that combine different active sites such as acidic and metallic components within a single nanostructure. This integrated design enables cascade reactions capable of directly transforming raw biomass components or intermediate compounds into targeted biofuel and pharmaceutical precursors through streamlined reaction sequences, thereby significantly improving process intensification [194].

Further progress in catalyst design, synthesis, characterization, and reactor engineering is essential for moving nanocatalysts from laboratory-scale potential to reliable industrial processes. Such advances will improve the sustainability and economic viability of multi-product biorefineries [192].

6. Synergistic Optimization via Computer-Aided Design

The complexity inherent in biological systems and integrated biorefinery processes requires advanced tools for analysis, prediction, and optimization, particularly when targeting the synergistic co-production of multiple products like biofuels and pharmaceuticals [195]. Computer-aided design (CAD) offers such a framework. It includes a wide range of computational modeling, simulation, and data analysis techniques to handle this complexity [196]. By creating mathematical models of metabolic networks, genetic circuits, enzyme kinetics, reactor dynamics, and downstream processes, CAD tools allow researchers to conduct in silico experiments. These tools help test hypotheses, identify bottlenecks, predict outcomes of genetic or environmental changes, and guide the rational design of improved strains and processes [197].

As systematically summarized in

Table 5. Examples of computer-aided design applications in co-production optimization.

Computational Tool/Method	Biological System/Process Targeted	Role in Optimizing Co-production	Refs.
Genome-Scale Metabolic Models (GEMs)	Whole-cell metabolism (bacteria, yeast, algae, etc.)	Comprehensive representation of metabolic network; Foundation for constraint-based modeling and systems analysis.	[204,205,206,207,208,209]
Flux Balance Analysis (FBA) and Variants (OptFlux, FVA)	Microbial metabolic flux distribution	Predicting optimal flux patterns; Identifying gene modification targets (knockouts, overexpression) for redirecting flux towards simultaneous biofuel/pharma production.	[210,211,212,213]
13C-Metabolic Flux Analysis	Intracellular metabolic fluxes	Quantifying actual metabolic fluxes to validate and refine GEMs and FBA predictions for co-production pathways.	[214,215,216]
Pathway Design Algorithms (e.g., RetroPath, BNICE)	Novel metabolic pathway construction	Designing synthetic pathways for target molecules; Exploring alternative routes; Identifying pathways potentially favoring co-production economics.	[217,218,219]
Molecular Dynamics Simulation	Enzyme structure function, Enzyme–substrate interactions	Understanding enzyme mechanisms; Guiding protein engineering efforts to improve catalyst efficiency or specificity relevant to biofuel/pharma synthesis.	[220,221,222,223]
Process Simulation Software (e.g., Aspen, SuperPro)	Integrated biorefinery processes (upstream, fermentation, downstream)	Designing, optimizing, and scaling up entire processes; Performing techno-economic analysis and life cycle assessment of co-production scenarios.	[224,225,226]
Machine Learning (ML)/Artificial Intelligence (AI)	Multi-omics data, Fermentation data, Genetic circuit design	Building predictive models from complex data; Optimizing conditions; Discovering enzyme functions; Designing dynamic control systems for balancing co-production.	[227,228,229,230,231]

, a diverse toolkit of computational methodologies is actively employed to optimize various aspects of biofuel and pharmaceutical co-production. At the core of metabolic engineering efforts are Genome-Scale Metabolic Models (GEMs), which represent the entire known metabolic reaction network of an organism [198]. Coupled with constraint-based modeling techniques like Flux Balance Analysis, GEMs enable the prediction of metabolic flux distributions under pseudo-steady-state conditions by optimizing objective functions such as biomass growth or product synthesis, while adhering to stoichiometric and thermodynamic constraints. Flux Balance Analysis and its many computational extensions, including OptFlux, Flux Variability Analysis, Minimization of Metabolic Adjustment, and Regulatory Flux Balance Analysis, serve as powerful tools for determining optimal genetic modifications. These approaches systematically identify gene knockout, knockdown, or overexpression targets that effectively redirect carbon flux toward the co-production of valuable compounds, such as achieving balanced synthesis of lipids for biodiesel and isoprenoids for pharmaceutical applications in engineered microbial systems like yeast or E. coli [198,199]. Computational pathway design tools such as RetroPath, BNICE, and OptStoic play a crucial role in discovering and assessing novel biosynthetic routes. These algorithms can construct artificial pathways by combining enzymes from diverse organisms to synthesize target compounds that either do not occur naturally or require optimized reaction kinetics and thermodynamics. A particularly valuable application involves deliberately engineering pathways that promote efficient co-production through strategic utilization of shared metabolic intermediates [200,201]. At the system level, advanced process simulation platforms including Aspen Plus, SuperPro Designer, and CHEMCAD facilitate comprehensive modeling and optimization of integrated biorefineries. These tools enable detailed analysis of the complete production chain, from feedstock pretreatment and enzymatic hydrolysis through fermentation processes to the intricate downstream separation and purification sequences necessary for multi-product biorefinery operations. These simulations allow for techno-economic analysis and life cycle assessment early in the design phase, evaluating the economic viability, energy balance, and environmental footprint of different co-production scenarios and process configurations [8,202]. More recently, machine learning and artificial intelligence algorithms are finding increasing application [203]. Machine learning enables the development of predictive models by analyzing large, complex datasets obtained from high-throughput experiments, such as those establishing correlations between genetic variants or fermentation parameters and co-product yields. These computational approaches can optimize fermentation media and culture conditions, predict novel enzymatic activities from sequence information, and facilitate the design of advanced synthetic genetic circuits for dynamic metabolic control. Such intelligent systems could empower microbial cells to autonomously regulate the equilibrium between biofuel and pharmaceutical synthesis in response to intracellular or environmental stimuli [203].

Integrating computational approaches across the entire research and development process—from initial strain design to full-scale process simulation and economic analysis—can significantly speed up progress. This acceleration helps realize the major economic and sustainability benefits that integrated, multi-product biorefineries offer.

7. Co-Development of Extremophiles for Dual Applications

Extremophiles are organisms adapted to thrive in environments hostile to most life, such as those with extreme temperature variations represented by thermophiles and psychrophiles, pH extremes including acidophiles and alkaliphiles, high salinity environments inhabited by halophiles, elevated pressure conditions tolerated by piezophiles, or intense radiation. These organisms are a valuable bioresource for industrial biotechnology, including the integrated co-production of biofuels and pharmaceuticals [232]. Their unique adaptations often result from novel biochemical pathways, distinct biomolecules, and highly robust enzymes known as extremozymes. These extremozymes can remain active and stable under the harsh processing conditions often found in industry [233,234].

The potential of extremophiles for simultaneous biofuel and pharmaceutical production is exemplified by various groups.

Table 6. Examples of extremophile co-development for dual applications.

Extremophile Type/Example	Extreme Condition Tolerance	Biofuel Product/Process Contribution	Pharmaceutical/Value-Added Product/Enzyme	Refs.
Thermophilic Bacteria/Archaea (Clostridium, Caldicellulosiruptor, Thermoanaerobacterium)	High Temperature (>60 °C)	Ethanol, Hydrogen, Butanol (from lignocellulose via CBP); Reduced contamination	Thermostable enzymes (cellulases, xylanases, ligninases, amylases, proteases)	[194,241,242,243,244]
Halophili Algae (Dunaliella salina)	High Salinity (>10–30% NaCl)	Lipids (biodiesel precursor), Glycerol	β-carotene, Lutein	[26,245,246,247,248,249,250]
Halophilic Archaea (Halobacterium, Haloferax)	High Salinity (15%—saturation)	Lipids (potential), PHAs (bioplastics/biomedical), Gas vesicles (potential)	Bacterioruberin (C50 carotenoid antioxidant), Compatible solutes (ectoine, hydroxyectoine)	[251,252,253,254,255,256,257]
Psychrophilic Bacteria/Algae/Fungi	Low Temperature (<15 °C)	Lipids (biodiesel precursor-potential)	Polyunsaturated fatty acids, Cold-active enzymes (lipases, proteases, amylases)	[258,259,260,261]
Acidophilic Microorganisms (Acidithiobacillus)	Low pH (<3)	Biomining contribution (metal leaching-indirect)	Acid-stable enzymes, Unique metabolites	[262,263,264,265]
Alkaliphilic Microorganisms (Bacillus spp.)	High pH (>9)	Contribution to specific bioconversions	Alkali-stable enzymes (proteases, amylases for detergents), Unique metabolites	[266,267,268,269,270]

systematically summarizes representative extremophile species with demonstrated dual production capabilities, aligning their biotechnological applications with corresponding biochemical adaptations. Thermophilic bacteria and archaea, thriving at temperatures above 60 °C, are particularly attractive for processing lignocellulosic biomass. Organisms like Clostridium thermocellum, Caldicellulosiruptor species, and Thermoanaerobacterium saccharolyticum can directly ferment cellulose and hemicellulose components into biofuels such as ethanol or hydrogen at high temperatures, often in a process known as consolidated bioprocessing (CBP) which combines enzyme production, hydrolysis, and fermentation in a single step [66]. This high-temperature operation reduces contamination risks and can improve reaction kinetics. Crucially, these thermophiles are sources of highly thermostable enzymes, including cellulases, xylanases, ligninases, and amylases, which are themselves valuable products for various industrial applications, including biomass degradation, food processing, detergents, and potentially even pharmaceutical synthesis requiring robust catalysts. Halophilic microorganisms, which tolerate salt concentrations as high as saturation, offer distinct opportunities. Halophilic microalgae like Dunaliella salina are commercially cultivated in hypersaline ponds for their massive accumulation of β-carotene while also producing glycerol and lipids that could be targeted for biodiesel production [235]. Halophilic archaea, such as Halobacterium salinarum or Haloferax mediterranei, produce unique C50 carotenoids like bacterioruberin, exhibiting potent antioxidant activity potentially exceeding that of β-carotene [236]. They also synthesize osmoprotectants like ectoine, hydroxyectoine, and glycine betaine to maintain osmotic balance; these compounds are highly valuable as protein stabilizers and moisturizers in cosmetics and are explored for therapeutic applications [237]. Some haloarchaea also accumulate polyhydroxyalkanoates, biodegradable polyesters that can be considered bioplastics or potentially modified for drug delivery, alongside their potential role in biomass-for-energy schemes [238]. Psychrophilic microbes, found in permanently cold environments, produce lipases, proteases, and amylases that exhibit high catalytic activity at low temperatures [234]. This is advantageous for processes where heating is undesirable, such as food modification and detergent additives, or energetically costly [239]. While direct biofuel production at low temperatures is less common, these microbes can accumulate lipids rich in polyunsaturated fatty acids like EPA and DHA, which are high-value nutraceuticals, representing a potential co-product alongside cold-active enzymes [240]. Acidophiles and alkaliphiles, thriving at extreme pH values, similarly possess unique enzymes (e.g., pH-stable proteases, amylases) and metabolic capabilities that could be harnessed for specific biotransformations relevant to both biofuel upgrading and pharmaceutical synthesis under non-neutral pH conditions, potentially simplifying process integration or enabling novel reaction chemistries.

For certain industrial applications, the natural robustness, unique metabolic pathways, and production of extremozymes and novel bioactive compounds give extremophiles significant advantages over conventional mesophilic organisms [232]. Challenges remain, particularly in optimizing cultivation, developing genetic tools for non-model extremophiles, and scaling up processes [271]. Nevertheless, the vast untapped biodiversity in extreme environments represents a rich resource for future discoveries [272].

8. Integrated Utilization of Plant Secondary Metabolites

Plants are a primary source of biomass for biofuel production, mainly from lignocellulose or plant oils. At the same time, they produce a vast array of secondary metabolites. These compounds are not directly involved in primary growth but are vital for the plant’s defense, signaling, and adaptation. Many of these secondary metabolites—such as alkaloids, terpenoids, phenolics, and glycosides—have strong biological activities and are the basis for numerous pharmaceuticals, nutraceuticals, flavors, and fragrances.

As systematically summarized in

Table 7. Examples of integrated utilization of plant secondary metabolites.

Plant Source/Type	Primary Biomass Use (Biofuel Potential)	Secondary Metabolite(s)	Medicinal Application(s)/Potential Benefits	Refs.
Crop Residues (Corn Stover, Wheat Straw)	Cellulosic Ethanol, Biogas	Phenolic Acids, Flavonoids	Antioxidant, Anti-inflammatory	[277,278,279,280,281,282,283]
Artemisia annua	Lignocellulosic Biomass Residue (Post-extraction)	Artemisinin	Antimalarial	[284,285,286]
Taxus spp.	Lignocellulosic Biomass Residue (Needles/Bark, Post-extraction)	Paclitaxel	Anticancer	[287,288,289]
Rapeseed Meal (Post-oil extraction)	Animal Feed/Fertilizer/Potential Energy Recovery	Phenolic Compounds, Glucosinolates	Antioxidant, Potential anticancer (glucosinolate metabolites)	[290,291,292,293,294,295]
Soybean Meal (Post-oil extraction)	Animal Feed/Fertilizer/Potential Energy Recovery	Isoflavones, Saponins, Phenolic acids	Phytoestrogenic (hormone health), Antioxidant, Potential anticancer	[296,297,298,299,300,301]
Sunflower Meal (Post-oil extraction)	Animal Feed/Fertilizer/Potential Energy Recovery	Chlorogenic acid, Other phenolic compounds	Antioxidant, Anti-inflammatory	[302,303,304,305]
Dedicated Energy Crops (Switchgrass, Poplar)	Cellulosic Biofuels	Phenolics, Flavonoids, Terpenoids—varies	Varies (Antioxidant, Anti-inflammatory potential, requires investigation)	[306,307,308,309]
Tobacco (Nicotiana spp.—engineered)	Potential for Oil (biodiesel)/Biomass	Engineered production of specific proteins/antibodies	Therapeutic proteins (e.g., vaccines, antibodies)	[310,311,312]

with their corresponding biofuel pathways and secondary metabolites, the potential for integrated utilization is evident across various plant feedstocks, ranging from dedicated energy crops and agricultural residues to established medicinal plants and oilseed crops. Lignocellulosic biomass from agricultural residues (e.g., corn stover, wheat straw, rice husks) or forestry residues, primarily targeted for cellulosic ethanol or biogas production, is also a source of phenolic compounds [273]. During conventional pretreatment methods such as dilute acid treatment, alkaline processing, and steam explosion—all employed to disrupt plant cell wall structures for biofuel production—phenolic acids including ferulic acid and p-coumaric acid are liberated into hydrolysate streams. These compounds typically exist in esterified forms bound to hemicellulose or lignin components prior to pretreatment. These compounds possess antioxidant and anti-inflammatory properties and can potentially be recovered as co-products before or after sugar fermentation [146]. Dedicated energy crops, such as switchgrass (Panicum virgatum), miscanthus (Miscanthus × giganteus), or fast-growing trees like poplar (Populus spp.), selected for high biomass yield, also contain a profile of secondary metabolites (phenolics, flavonoids, terpenoids) that could potentially be extracted as value-added co-products, although research in this area is less developed than for residues or medicinal plants. Medicinal plants offer a clear case for integration; Artemisia annua, cultivated for the potent antimalarial sesquiterpene lactone artemisinin, generates significant amounts of residual lignocellulosic biomass after the primary drug extraction. Developing methods to efficiently convert this residue into biofuels would substantially improve the economics of artemisinin production and reduce waste. Similarly, the processing of Taxus species needles or bark for the widely used anticancer drug paclitaxel leaves behind large quantities of biomass residues that could potentially be valorized through biofuel conversion pathways. Oilseed crops, the primary source for biodiesel, provide another important example. After oil extraction from seeds like rapeseed, sunflower, or soybean, a protein-rich meal remains. This meal is not only valuable as animal feed but also contains bioactive secondary metabolites. Rapeseed meal contains significant amounts of phenolic compounds, particularly sinapic acid and its derivatives, known for antioxidant properties [274]. Soybean meal is rich in isoflavones, phytoestrogens extensively studied for their potential health benefits, including roles in cancer prevention and cardiovascular health [275]. Integrating the recovery of these bioactive compounds from the meal fraction before or alongside its use as feed could add significant value to the biodiesel production chain. Key technological challenges involve developing cost-effective, selective, and scalable extraction and purification methods (e.g., sequential extraction, solvent optimization, membrane filtration, chromatography) that are compatible with subsequent biofuel processing steps and maintain the integrity of both the secondary metabolites and the residual biomass [276].

A key principle demonstrated across diverse feedstocks is that synergistic benefits arise from a holistic biorefining approach [313]. Targeting both the structural carbohydrates or oils for biofuels and the diverse secondary metabolites for high-value applications significantly broadens the economic foundation for utilizing energy crops, agricultural and forestry residues, traditional medicinal plants, and oilseed crops alike.

9. Overarching Challenges and Future Prospects for Integrated Co-Production

Despite the significant potential outlined in previous sections, realizing the widespread industrial application of integrated biofuel–pharmaceutical co-production faces considerable hurdles across multiple domains. Successfully navigating these is key to unlocking the full benefits of this synergistic approach.

Technically, the core challenges lie in efficiently managing complex biological systems for dual outputs and integrating the downstream processing of multiple, often disparate products. Optimizing cellular metabolism to simultaneously achieve high yields for both low-volume, high-value pharmaceuticals and high-volume, lower value biofuels without significant trade-offs due to metabolic burden or precursor competition remains a central difficulty (Reference metabolic burden/yield challenge). Furthermore, developing cost-effective, integrated downstream processes capable of efficiently separating and purifying products with potentially very different physicochemical properties and required purity levels (fuel-grade vs. pharmaceutical-grade) is a major bottleneck requiring significant innovation [314].

Economically, the substantial capital investment needed for establishing complex integrated biorefineries, coupled with uncertainties in long-term feedstock supply and pricing, poses major barriers. Achieving overall process profitability hinges on demonstrating cost-competitiveness, particularly for the biofuel component against established fossil fuels, while simultaneously meeting the stringent quality and regulatory standards for the high-value pharmaceutical co-product [315]. Seufitelli et al. (2022) demonstrated an integrated poplar biorefinery that co-produced jet fuel, xylitol, and formic acid with superior economic performance [316]. At a 250 kton/year scale, co-product revenues enabled a competitive jet fuel price of USD 3.13/gallon (vs. Conventional E) [316]. The Swedish company Sekab utilizes its CelluAPP technology to produce bioethanol and chemicals for the pharmaceutical industry (such as acetaldehyde and ethyl acetate). Its demonstration plant has showcased the potential for processing complex biomass [317]. The Norwegian company Borregaard’s biorefinery produces bioethanol and lignin-based products (such as vanillin and microfibrillated cellulose), the latter of which are used in the pharmaceutical industry; its operations highlight the potential for co-production [318,319]. Biodiesel refineries can enhance economic viability by producing high-value chemicals like succinic acid, but this requires extensive optimization to offset high capital costs [320]. Companies such as Abengoa, DuPont, and M&G abandoned their cellulosic ethanol plants before 2018 due to economic challenges, reflecting the profitability hurdles in the biofuel sector [321].

From a regulatory and societal perspective, clear, science-based, and internationally consistent frameworks are needed for the assessment and deployment of genetically modified organisms, especially those developed using advanced synthetic biology tools. Building public trust and market acceptance for novel bio-based processes and products through transparency and engagement is also crucial [322,323].

Nevertheless, continued progress across several key areas offers promising avenues to overcome these obstacles. Advances in synthetic biology and metabolic engineering provide increasingly powerful tools for designing and controlling complex cellular pathways with greater precision and efficiency. Systems biology approaches, integrating multi-omics data with computational modeling, deepen our understanding of cellular processes, enabling more predictive design and optimization. Concurrently, innovations in bioprocess engineering, focusing on process intensification and novel, selective separation technologies, are vital for improving scalability and reducing costs [324,325]. Performing rigorous techno-economic and life-cycle assessments throughout development is essential to guide research towards genuinely sustainable and viable configurations. Finally, fostering strong interdisciplinary collaborations and establishing supportive, stable policy environments that incentivize sustainable bio-based production are fundamental requirements for accelerating the transition from laboratory potential to industrial reality. Addressing these multifaceted challenges through concerted innovation holds the key to fully realizing the significant societal benefits offered by integrated biofuel–pharmaceutical co-production.

A particularly critical regulatory challenge lies in pharmaceutical Good Manufacturing Practice (GMP) compliance throughout production processes to ensure product quality and safety. The integration of GMP-compliant processes within biorefinery operations for simultaneous industrial chemical and pharmaceutical manufacturing presents multifaceted obstacles: It necessitates establishing independent quality management systems and dedicated facilities, substantially increasing capital and operational expenditures. Implementation of full-process traceability from raw materials to finished products becomes imperative to guarantee batch-to-batch consistency in co-produced pharmaceuticals. Three primary risk categories demand rigorous control in co-production systems: (1) comprehensive characterization of co-products (e.g., microbial metabolites, plant secondary metabolites), requiring thorough analysis of process residuals from biofuel operations such as lignin derivatives and nanoscale catalysts; (2) stringent evaluation of engineered biologics (e.g., therapeutic proteins from extremophiles) for immunogenicity and stability; and (3) regulatory compliance for genetically modified organisms (e.g., CRISPR-edited microbial strains), mandating adherence to compliance with specific genetically modified organism (GMO) regulations and elimination of genotoxic contaminants. Given pharmaceutical development cycles spanning 10–15 years with substantial clinical trial investments, the economic viability of co-production models becomes acutely dependent on production costs and market demand, while demanding biorefinery operators’ capacity to anticipate evolving regulatory landscapes. Regulatory pathways diverge significantly across co-product categories: biological products (e.g., insulin precursors from engineered yeast, therapeutic antibodies from transgenic tobacco plants) require Biologics License Applications (BLAs) through multistage clinical trials under FDA’s Center for Biologics Evaluation and Research (CBER) or European Medicines Agency (EMA) oversight [326]. Co-products meeting biosimilar criteria may leverage EMA’s abbreviated clinical trial requirements under recent guidelines. Meanwhile, bio-based chemical intermediates serving as pharmaceutical precursors (e.g., butanediol, lactic acid) primarily fall under industrial chemical regulations, though final drug products must still comply with stringent pharmacopeial standards [327].

10. Conclusions

Integrated co-production of biofuels and pharmaceuticals is a highly promising, synergistic strategy that uses biological systems to sustainably address global energy and health needs. Key approaches discussed include exploiting versatile microbial metabolites; harnessing the power of synthetic biology to engineer custom production platforms; and valorizing biorefinery waste streams into medicinal compounds. Moreover, applying advanced nanocatalysts, utilizing the potential of extremophiles, integrating plant secondary metabolites, and using computer-aided design to optimize complex interactions further illustrate the field’s multifaceted nature. These multifaceted strategies are further contextualized in Figure 2, which suggests critical future research directions to advance this field. Significant technical, economic, and regulatory challenges remain. However, future directions based on systems biology, process intensification, robust strain development, and supportive policies are set to unlock co-production’s substantial potential. Through continued interdisciplinary innovation and collaboration, this field can significantly contribute to a circular bioeconomy, energy security, and the discovery of novel therapeutics.