Biology subjects

Rahimi, A.

Publications and source records attributed to Rahimi, A..

15 recordsLinked to original sources

bioRxiv2026

Pan-Coronavirus Protease Engagement and Differentiated Pharmacology of Antiviral Candidate CMX990

COVID-19 highlighted the need for antivirals that can be rapidly deployed against both current and future coronavirus threats. CMX990 is a clinical stage coronavirus main protease (Mpro) inhibitor bearing a unique trifluoromethoxymethyl ketone warhead. Here, we broadly evaluate its pan-coronavirus target engagement, antiviral breadth, and pharmacologic differentiation. Across a reporter panel of 24 Mpro enzymes spanning alpha-, beta-, delta-, and gamma-coronaviruses, CMX990 retained robust potent activity, including against nirmatrelvir-resistant SARS-CoV-2 variants. In direct comparison, nirmatrelvir and ensitrelvir showed diminished potency against non-SARS-CoV-2 coronaviruses. Live-virus assays corroborated this breadth, with potent, selective activity against SARS-CoV-2, SARS-CoV-1, MERS-CoV, and additional human coronaviruses. Structural studies revealed a conserved covalent binding mode centered on the catalytic Cys of coronavirus Mpro. In serial-passage studies, resistance emerged only after approximately twice as many serial passages under CMX990 selection as under nirmatrelvir selection, without selecting for the canonical nirmatrelvir-resistance substitution E166V. Extracellular washout experiments revealed superior persistence of antiviral activity relative to nirmatrelvir, consistent with durable target engagement. In a murine SARS-CoV-2 infection model, once-daily CMX990 protected against weight loss and reduced lung viral titers to near baseline levels. Collectively, these findings identify CMX990 as a structurally and functionally validated pan-coronavirus protease inhibitor supporting its potential as a pandemic-ready antiviral candidate.

pharmacology and toxicology↗

bioRxiv2026

Orally Bioavailable SARS-CoV-2 Protease Inhibitors Bearing a Hydroxymethyl Ketone Warhead

The use of covalent warheads targeting the catalytic cysteine has been a cornerstone in coronavirus main protease (Mpro) inhibitor development, where various electrophilic motifs have been used including aldehydes, nitriles, ketoamides, and hydroxymethyl ketones (HMKs). Recent efforts have been mostly centered around nitrile warheads, given the success of compounds like Nirmatrelvir and Ensitrelvir in the clinic. However, finding and advancing alternative chemotypes with differentiating chemical and pharmacological profiles is essential for future pandemic preparedness. Among such alternatives, HMKs hold special interest because they balance reduced intrinsic electrophilicity with an excellent selectivity profile. Nevertheless, early HMK-based compounds, such as the clinical-stage Mpro inhibitor PF-00835231, suffered from poor oral bioavailability and therefore required intravenous administration, with or without prodrug derivatization of the hydroxyl group. Here, we describe our efforts in advancing the HMK field via the discovery of mCMX110, a lead that has superior potency, increased unbound exposure in vivo, and favorable oral bioavailability in preclinical studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/725542v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@40222aorg.highwire.dtl.DTLVardef@831b88org.highwire.dtl.DTLVardef@184a910org.highwire.dtl.DTLVardef@779095_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2023

Discovery of CMX990: A Potent SARS-CoV-2 3CL Protease Inhibitor Bearing a Novel Covalent Warhead

There remains a need to develop novel SARS-CoV-2 therapeutic options that improve upon existing therapies by increased robustness of response, fewer safety liabilities, and global-ready accessibility. Functionally critical viral main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target due to its homology within the coronaviral family, and lack thereof towards human proteases. In this disclosure, we outline the advent of a novel SARS-CoV-2 3CLpro inhibitor, CMX990, bearing an unprecedented trifluoromethoxymethyl ketone warhead. Compared with the marketed drug nirmatrelvir (combination with ritonavir = PaxlovidTM), CMX990 has distinctly differentiated potency ([~]5x more potent in primary cells) and human in vitro clearance (>4x better microsomal clearance and >10x better hepatocyte clearance), with good in vitro-in vivo correlation. Based on its compelling preclinical profile and projected once or twice a day dosing supporting unboosted oral therapy in humans, CMX990 advanced to a Phase 1 clinical trial as an oral drug candidate for SARS-CoV-2.

microbiology↗

bioRxiv2022

Potassium homeostasis and signaling as a determinant of Echinacea species tolerance to salinity stress

Salt tolerant is strongly related to potassium (K+) retention in plant tissues under salt stress conditions. However, it is unclear for different Echinacea species. So, mechanistic basis of four Echinacea species (i.e. Echinacea purpurea, Echinacea angustifolia, Echinacea pallida, and Echinacea sanguinea) to salinity stress tolerance, and K+ retention were assessed in the present study. Non-invasive microelectrode ion flux measuring, DHAR and MDHAR activities, and pharmacological measurements were performed based on the standard methods. Ion flux measurements revealed higher K+ efflux in E. pallida and E. sanguinea species compared to the E. purpurea and E. angustifolia species in the elongation zone. Higher salinity-induced H+ efflux was found in the elongation zone than mature zone. However, E. angustifolia and E. purpurea had more Ca2+ influx compared to E. pallida and E. sanguinea species. Net K+ efflux decreased (> 90%) in the presence of TEA and GdCl3. Increasing of Ca2+ uptake and K+ loss in four Echinacea species roots were found in the presence of 0.3 mM Cu/Ascorbate (Cu/Asc). The significant role of H+-ATPase in H+ efflux was demonstrated by Sodium orthovanadate. Ultimately, the physiological properties of Echinacea species have a critical role in salinity-resistant/sensitive differences. Future scientific understanding of Echinacea species physiognomies may be necessary for better understanding of the plant behavior to salinity stress. One-sentence summaryHigher K+ efflux in E. pallida and E. sanguinea species as a result of NaCl and ROS act as a metabolic switch to save energy for adaptations and repairs in salinity stress conditions.

plant biology↗

bioRxiv2022

Key role of auxin cellular accumulation in totipotency and pluripotency acquisition

Genome editing and in vitro based-plant propagation require efficient plant regeneration system. Somatic embryogenesis (SE) or de novo shoot regeneration are two major systems that widely used for plant in vitro regeneration. Most SE or shoot regeneration protocols rely on the exogenous application of the synthetic auxin analog 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthylene acetic acid (NAA), whereas the natural auxins indole-3-acetic acid (IAA), 4-chloroindole-3-acetic acid (4-Cl-IAA) or indole-3-butyric acid (IBA) are not or less effective for plant regeneration. Although these synthetic auxins mimics the physiological activity of the main natural auxin IAA in many aspects, there are also clear differences that have been attributed to differences in stability or to different affinities for certain TIR1/AFB-Aux/IAA auxin co-receptor pairs. Here we show that the success of 2,4-D in inducing SE from Arabidopsis is related to ineffectiveness as substrate for auxin efflux, resulting in its intracellular 2,4-D accumulation. Reducing auxin efflux by addition of the auxin transport inhibitor naphthylphthalamic acid (NPA) also allowed natural auxins and other synthetic analogs to induce SE in Arabidopsis with similar efficiencies as 2,4-D. The PIN-FORMED auxin efflux carriers PIN1, PIN2 and the ATP-binding cassette-B auxin transporters ABCB1 and ABCB19 were shown to be partially responsible for the efflux of natural auxins during SE induction. Importantly, all somatic embryos induced in Arabidopsis by IAA in the presence of NPA showed a normal embryo to seedling conversion and subsequent plant development, whereas for the 2,4-D system this was limited to 50-60% of the embryos. We showed that the auxin transport inhibition promotes de novo shoot regeneration capacity from callus induced by 4-Cl-IAA in Brassica napus. In addition, we observed a obvious acceleration in shoot bud emerging from callus induced by 4-Cl-IAA than 2,4-D. Based on our data we conclude, that the efficiency of plant propagation can be significantly improved by applying the natural auxins in the presence of the auxin transport inhibitor NPA.

plant biology↗

bioRxiv2021

Endogenous auxin directs development of embryonic stem cells into somatic proembryos in Arabidopsis

Somatic embryogenesis (SE) is the process by which embryos develop from in vitro cultured vegetative tissue explants. The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is widely used for SE induction, but SE can also be induced by overexpression of specific transcription factors, such as AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15). 2,4-D and AHL15 both trigger the biosynthesis of the natural auxin indole-3-acetic acid (IAA). However, the role of this endogenously produced auxin in SE is yet not well understood. In this study we show that the induction of embryonic stem cells from explants does not require IAA biosynthesis, whereas an increase in IAA levels is essential to maintain embryo identity and for embryo formation from these stem cells. Further analysis showed that YUCCA (YUC) genes involved in the IPyA auxin biosynthesis pathway are up-regulated in embryo-forming tissues. Chemical inhibition of the IPyA pathway significantly reduced or completely inhibited the formation of somatic embryos in both 2,4-D-and AHL15-dependent systems. In the latter system, SE could be restored by exogenous IAA application, confirming that the biosynthesis-mediated increase in IAA levels is important. Our analyses also showed that PIN1 and AUX1 are the major auxin carriers that determine respectively auxin efflux and influx during SE. This auxin transport machinery is required for the proper transition of embryonic cells to proembryos and, later, for correct cell fate specification and differentiation. Taken together, our results indicate that auxin biosynthesis in conjunction with its polar transport are required during SE for multicellular somatic proembryo development and differentiation. One sentence summarySomatic embryogenesis in Arabidopsis requires auxin biosynthesis and polar auxin transport only after the acquisition of embryonic competence for somatic proembryo development and differentiation.

plant biology↗

bioRxiv2020

miR156-independent repression of the ageing pathway bylongevity-promoting AHL proteins in Arabidopsis

Plants age by transition through distinct developmental phases, with the juvenile- to adult vegetative and the adult vegetative to reproductive phase change as two consecutive important post-embryonic phase transitions. During the transition from the juvenile- to adult vegetative phase, also known as the vegetative phase change (VPC), many plants undergo specific morphological and physiological changes. In the model plant Arabidopsis thaliana (Arabidopsis), for example, the VPC is marked by clear heteroblastic changes in leaf shape and size and the appearance of trichomes on the abaxial side of leaves. The VPC and the vegetative to reproductive transition are promoted by the SQUAMOSA PROMOTOR BINDING PROTEIN-LIKE (SPL) family of transcription factors and repressed by miR156 and miR157 that target the SPL transcripts. Here we present data that the plant longevity promoting AT-HOOK MOTIF NUCLEAR LOCALIZED protein 15 (AHL15) and family members also repress the SPL-driven ageing pathway. Arabidopsis ahl loss-of-function mutants showed an accelerated VPC and flowering time, whereas AHL15 overexpression dramatically delayed the VPC and flowering time in both Arabidopsis and Nicotiana tabacum. Expression analysis and tissue-specific AHL15 overexpression revealed that AHL15 affects the VPC and flowering time directly through its expression in the shoot apical meristem and young leaves. In addition, we found evidence that AHL15 represses SPL gene expression in a miR156/157-independent manner. The juvenile traits of spl loss-of-function mutants appeared to be dependent on the enhanced expression of the AHL15 gene, providing evidence for a reciprocal negative feedback between AHL15 and SPL genes. Antagonistically to AHLs, SPLs promote axillary meristem (AM) maturation and thus prevent vegetative growth from these meristems by repressing AHL15 expression. Taken together, our results place AHL15 and family members at a central position in the SPL-driven ageing pathway as suppressors of the VPC, flowering time and AM maturation.

plant biology↗

bioRxiv2020

A novel pathway controlling cambium initiation and -activity via cytokinin biosynthesis in Arabidopsis

Plant secondary growth, also referred to as wood formation, includes the production of secondary xylem, which is derived from meristematic cambium cells embedded in vascular tissues. Despite the importance of secondary xylem in plant growth and wood formation, the molecular mechanism of secondary growth is not yet well understood. Here we identified an important role for the Arabidopsis thaliana (Arabidopsis) AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15) gene, encoding for a putative transcriptional regulator, in controlling vascular cambium activity and secondary xylem formation. Secondary xylem development was significantly reduced in inflorescence stems of the Arabidopsis ahl15 loss-of-function mutant, whereas AHL15 overexpression led to extensive secondary xylem formation. AHL15 expression under a vascular meristem-specific promoter also enhanced the amount of interfascicular secondary xylem. Moreover, AHL15 appeared to be required for the enhanced secondary xylem formation in the Arabidopsis double loss-of-function mutant of the SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FRUITFULL (FUL) genes. A well-known central regulator of cambial activity is the plant hormone cytokinin. We showed that the expression of two cytokinin biosynthesis genes (ISOPENTENYL TRANSERASE (IPT) 3 and 7) is decreased in ahl15 loss-of-function mutant stems, whereas the secondary xylem deficiency in these mutant stems can be resorted by cambium-specific expression of the Agrobacterium tumefaciens IPT gene, indicating that AHL15 acts through the cytokinin pathway. These findings support a model whereby AHL15 acts as a central factor inducing vascular cambium activity downstream of SOC1 and FUL and upstream of IPT3, IPT7 and LOG4, LOG5 governing the rate of secondary xylem formation in Arabidopsis inflorescence stems.

plant biology↗

bioRxiv2020

Gene Expression Signature and Molecular Mechanism of Redox Homeostasis in Colorectal Cancer

Cellular redox homeostasis is the important tool for normal cell function and survival. Oxidants, reductants and antioxidants are the players to maintain cellular homeostasis balance. However, in some conditions like cancer, the concentration and activation of these players are disturbed. This study walks you through the molecular mechanism of redox homeostasis to describe how expression level of these players would help colorectal cancer (CRC) cells continue proliferation and survive in the hypoxic environment of tumor. We proposed that O2- concentration is not detrimentally high in CRC cells since expression level of MnSOD didnt change noticeably. We also suggested that High proliferative CRC cells obtain their energy by oxidation of H2S in or Electron transport chain (ETC) and keep the adequate concentration of H2S by diminishing the expression level of enzymes involved in sulfide oxidation pathway. Reduction in hydrogen sulfide oxidation results in a decrease in the level of GSH. Glutathione peroxidase enzyme requires GSH to convert H2O2 into oxygen and water. Therefore, Level of hydrogen peroxide stays high which leads to an increase in cell proliferation. Furthermore, we analyzed the expression level of transcription factors sensitive to redox messengers.

systems biology↗

bioRxiv2020

Systems Biomedicine of Colorectal Cancer Reveals Potential Targets for CRC treatment

Colorectal cancer (CRC) is one of the major causes of cancer deaths across the world. Patients survival time at time of diagnosis depends largely on stage of the tumor. Therefore, understanding the molecular mechanisms promoting cancer progression from early stages to high-grade stages is essential for implementing therapeutic approaches. To this end, we performed a unique meta-analysis flowchart by identifying differentially expressed genes (DEGs) between normal, primary and metastatic samples in some test datasets. DEGs were employed to construct a protein-protein interaction (PPI) network. Then, a smaller network containing 39 DEGs were extracted from the PPI network whose nodes expression induction or suppression alone or in combination with each other would inhibit tumor progression or metastasis. A number of these DEGs were then verified by gene expression profiling, survival analysis and a number of validation datasets from different genomic repositories. They were involved in cell proliferation, energy production under hypoxic conditions, epithelial to mesenchymal transition (EMT) and angiogenesis. Multiple combination targeting of these DEGs were proposed to have high potential in preventing cancer progression. Some genes were also presented as diagnostic biomarkers for colorectal cancer. Finally, TMEM131, DARS and SORD genes were identified in this study which had never been associated with any kind of cancer neither as a biomarker nor curative target.

systems biology↗

bioRxiv2020

Pathway Mining and Data Mining in Functional Genomics. An Integrative Approach to Delineate Boolean Relationships Between Src and Its targets

MotivationThere are important molecular information hidden in the ocean of big data could be achieved by recognizing true relationships between different molecules. Human mind is very limited to find all molecular connections. Therefore, we introduced an integrated data mining strategy to find all possible relationships between molecular components in a biological context. To demonstrate how this approach works, we applied it on proto-oncogene c-Src. ResultsHere we applied a data mining scheme on genomic, literature and signaling databases to obtain necessary biological information for pathway inference. Using R programming language, two large edgelists were constructed from KEGG and OmniPath signaling databases. Next, An R script was developed by which pathways were discovered by assembly of edge information in the constructed signaling networks. Then, valid pathways were distinguished from the invalid ones using molecular information in articles and genomic data analysis. Pathway inference was performed on predicted pathways starting with Src and ending with the DEGs whose expression were affected by c-Src overactivation. Moreover, some positive and negative feedback loops were proposed based on the gene expression results. In fact, this simple but practical flowchart will open new insights into interactions between cellular components and help biologists look for new possible molecular relationships that have not been reported neither in signaling databases nor as a signaling pathway.

bioinformatics↗

bioRxiv2020

An Arabidopsis AT-hook motif nuclear protein mediates somatic embryogenesis and coinciding genome duplication

Plant somatic cells can be reprogrammed to totipotent embryonic cells that are able to form differentiated embryos in a process called somatic embryogenesis (SE), by hormone treatment or through overexpression of certain transcription factor genes, such as BABY BOOM (BBM). Here we show that overexpression of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15) gene induces formation of somatic embryos on Arabidopsis thaliana seedlings in the absence of hormone treatment. During zygotic embryogenesis, AHL15 expression starts early in embryo development, and AH15 and other AHL genes are required for proper embryo patterning and development beyond the heart stage. Moreover, AHL15 and several of its homologs are upregulated and required for SE induction upon hormone treatment, and they are required for efficient BBM-induced SE as downstream targets of BBM. A significant number of plants derived from AHL15 overexpression-induced somatic embryos are polyploid. Polyploidisation occurs by endomitosis specifically during the initiation of SE, assumingly due to AHL15-mediated heterochromatin decondensation coinciding with the acquisition of embryonic competency in somatic plant cells.

plant biology↗

bioRxiv2020

A suppressor of axillary meristem maturation promotes longevity in flowering plants

Post embryonic development and growth of flowering plants are for a large part determined by the activity and maturation state of stem cell niches formed in the axils of leaves, the so-called axillary meristems (AMs)1,2. Here we identify a new role for the Arabidopsis AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15) gene as a suppressor of AM maturation. Loss of AHL15 function accelerates AM maturation, whereas ectopic expression of AHL15 suppresses AM maturation and promotes longevity in Arabidopsis and tobacco. Together our results indicate that AHL15 expression acts as a key molecular switch, directly downstream of flowering genes (SOC1, FUL) and upstream of GA biosynthesis, in extending the plants lifespan by suppressing AM maturation.

plant biology↗

bioRxiv2019

High-yield Production of Recombinant Platelet Factor 4 Protein by Harnessing and Honing the Gram-negative Bacterial Secretory Apparatus

BackgroundPlatelet factor 4 is a cytokine released into the bloodstream by activated platelets and plays a pivotal role in heparin-induced thrombocytopenia etiology and diagnosis. Therefore, a sustainable source of recombinant PF4 with structural and functional similarity to its native form is urgently needed to be used in diagnostic procedures. To this end, a three-in-one primary construct was designed and custom synthesized based on the pET26b backbone from which three secondary constructs could be derived each capable of employing either type I, type II secretory or cytoplasmic pathways. Protein expression and secretion were performed in Escherichia coli BL-21 (DE3) and were confirmed by SDS-PAGE and Western blotting. To further enhance protein secretion, the effect of several controllable factors including IPTG, Triton X-100, Sucrose, and Glycine were individually investigated at first. In the next step, according to fractional factorial approach, the synergistic effect of IPTG, Triton X-100, and Glycine on secretion was further investigated. To ascertain the structure and function of the secreted recombinant proteins, Dynamic light scattering was utilized and confirmed rPF4 tetramerization and heparin-mediated ultra-large complex formation. Moreover, Raman spectroscopy was exploited to determine the rPF4 secondary structure. ResultsType II secretory pathway was proven to be superior over type I in case of rPF4 secretion into the extracellular milieu. Protein secretion mediated by Type II was enhanced to approximately more than 700 g/ml. Large quantities of native rPF4 up to 20 mg was purified upon a minor scale up to 40 ml of culture medium. Dynamic light scattering unveiled native rPF4 quaternary structure revealing the formation of tetramers having an average size of 10 nm and formation of larger complexes of approximately 100-1200 nm in size following heparin supplementation, implying proper protein folding, tetramerization, and antigenicity. Analysis of the Zeta potential on approximately 600 g/ml of rPF4 revealed a 98 mV positive charge which further confirms protein folding. Moreover, rPF4 secondary structure was determined to be 43.5% Random coil, 32.5% {beta}-sheet, 18.6 % -helix and 4.9 % Turn, which is in perfect agreement with the native structure. Conclusionour results indicate that the gram-negative type II bacterial secretory system holds a great promise to be employed as a reliable protein production strategy with favorable industrial application. However, further efforts are required to realize the full potential of secretory pathways regarding their application to proteins with distinct characteristics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/830851v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@fd47fdorg.highwire.dtl.DTLVardef@8163c3org.highwire.dtl.DTLVardef@bcbb5eorg.highwire.dtl.DTLVardef@b145d5_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract. rPF4 secretion mediated by type 2 secretory system. The pelB signal sequence directs protein export into the extracellular milieu through the SecYEG translocon complex in a process assisted by SecB chaperone. A) Indicates protein secretion before supplementation with additives and B) indicates secretion in the presence of additives. C_FIG

bioengineering↗

bioRxiv2018

Analysis of a Novel Bioreactor Designed for Ultrasound Stimulation of Cell-Seeded Scaffolds

Although daily low intensity pulsed ultrasound (LIPUS) treatment has been shown to induce cellular responses supporting bone repair, in vitro studies in 3D models, such as cell-seeded scaffolds, are needed to further investigate the underlying cellular mechanisms. This requires well-controlled conditions in an US bioreactor. Computational studies are needed to investigate various effects on US wave propagation influenced by bioreactor configurations, such as reflections at interfaces and wave interference, and optimize the bioreactor design for experimental repeatability. In this study, an enclosed cylindrical sample holder that contained an inner well for placement of a scaffold immersed in culture medium was fabricated by stereolithography 3D printing and combined with an acoustic absorbent material to eliminate the presence of an air-liquid interface perpendicular to the wave propagation path. Finite element simulations conducted in the frequency domain demonstrated that weak standing waves were present within the culture medium, indicating the effects of reflections at solid-liquid interfaces within the sample holder, as expected. Focusing on the acoustic pressure at the inner well surface, it was found that the spatially-averaged pressure varied from a maximum to a minimum value as the thickness of the water layer beneath the sample holder was changed. Average pressure values at antinode positions were 2-fold higher than at node positions. A volume-averaged pressure was calculated within the culture medium corresponding to the region where a scaffold would be centrally located within the bioreactor. It was shown that the thickness of the volume analyzed had a minimal effect on the calculated average pressure. Time-dependent simulations for one complete pulse (i.e. 1 ms) showed that the acoustic pressure in volumes that would be occupied by scaffolds of two different thicknesses (diameter of 8.5 mm and thicknesses of 0.2 or 2.0 mm) reached a stable value after 45 {micro}s, and then remained at that value until the active period of the pulse ceased. Once the active period ended, the acoustic pressure rapidly decreased to a low baseline pressure. Overall, this study showed that the proposed novel bioreactor design provided a controlled environment for the US treatment of a cell-seeded scaffold by removing the air-liquid interface using a custom-designed sample holder and an acoustic absorbent material.

bioengineering↗