WO2023281523A1

WO2023281523A1 - A pharmaceutical composition with a recombinant fragment of human surfactant protein-d for sars-cov-2 infection

Info

Publication number: WO2023281523A1
Application number: PCT/IN2022/050237
Authority: WO
Inventors: Taruna Madan; Uday Kishore; Hrishikesh Pandit; Rambhadur SUBEDI; Susan IDICULA-THOMAS; Indra KUNDU; Barnali BISWAS
Original assignee: Indian Council Of Medical Research
Priority date: 2021-07-09
Filing date: 2022-03-15
Publication date: 2023-01-12

Abstract

The present disclosure relates to a pharmaceutical composition comprising of 2-75% recombinant fragment of human surfactant protein D (rfhSP-D) of SEQ ID NO. 2; and 0.05-2.0% CaCl2; effective against pulmonary infection, including SARS-CoV-2. The composition prepared is a nebulizer or dry powder composition. The present composition is useful as a monotherapy or an adjunct therapy against pulmonary infection caused by SARS-CoV-2.

Description

A PHARMACEUTICAL COMPOSITION WITH A RECOMBINANT FRAGMENT OF HUMAN SURFACTANT PROTEIN-D FOR SARS-COV-2 INFECTION

FIELD OF THE INVENTION

[001] The present disclosure relates to pharmaceutical compositions. More particularly, the present disclosure relates to a pharmaceutical composition comprising essentially recombinant fragment of human Surfactant Protein D (rfhSP-D) and calcium chloride as monotherapy or an adjunct therapy against pulmonary infection caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2).

BACKGROUND OF THE INVENTION

[002] Human surfactant protein D (SP-D) is a host defense, innate immune molecule that identifies molecular patterns on pathogens. Binding of SP-D to envelopes of viruses such as Influenza A Virus (IAV), Respiratory Syncytial Vims (RSV) and Human Immunodeficiency Vims (HIV) leads to agglutination of the vims.

[003] Surfactant Protein D (SP-D) is a hydrophilic component of lung surfactant with critical roles in maintenance of surface tension at the air-alveolar interface and in host defense. It is a C-type lectin comprising of collagen domain secreted by type II clara cells (alveolar epithelial cells), with a calcium ion dependent pattern recognition ability. Being a calcium-dependent lectin, SP-D binds maltose, glucose, mannose, fucose, galactose, lactose, glucosamine, and N-acetylglucosamine, and to complex carbohydrates on the surface of several pathogens (Madan and Kishore, 2020).

[004] SP-D is produced by different cell types, including type II pneumocytes, non-ciliated bronchiolar cells, submucosal gland and epithelial cells of trachea in the lung. Other sources include ductal epithelial cells in the lacrimal apparatus, mucosal and glandular/ductal epithelial cells in the gastrointestinal tract, skin, male and female genitourinary tracts (Madsen et ah, 2000). Vascular endothelial cells in heart and brain tissues also synthesize significant levels of SP-D. Such a widespread existence of SP-D in various tissues and fluids and its increased expression in response to pathogens emphasizes its important as an innate immune surveillance molecule at the mucosal barriers.

[005] The mechanism of action of SP-D resides in its dual interaction. It has a carbohydrate recognition domain (CRD) that bind specifically to exposed carbohydrate residues on the surface of the microorganisms and a collagen domain that interacts with various innate immunity cells such as macrophages, dendritic cells, lymphocytes, eosinophils etc. This property has led to its therapeutic application in various animal models for bacterial, viral and fungal infections. The therapeutic potential of collectins for example-SP-D in infection, inflammation and their regulatory role in innate immunity has been well researched and documented (Madan et al, 1997).

[006] Severe acute respiratory syndrome (SARS) is an acute pulmonary disease characterized by inflammation and immunological injury (Lang et al, 2003). It is highly transmissible via the respiratory route and has been attributed to pulmonary infection caused by corona virus-2 (CoV-2). Coronaviruses are positive- stranded RNA viruses with genomes of ~30 kb in size (Enjuanes et al, 2001). Sequencing of its genome shows that SARS-CoV-2 expresses the spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins. The Spike protein (S), a 1255 amino acid glycoprotein precursor present on the envelope of SARS- CoV-2, interacts with ACE2 protein on human cells via Receptor Binding Domain (RBD) present in S 1 subunit and facilitates viral entry into the Type II alveolar cells present in the lung. Spike protein of SARS-CoV-2 is activated by protease TMPRSS2 before it binds to ACE-2 via RBD.

[007] Leth-Larsen et al, 2007 teaches SP-D binding to Receptor binding domain (RBD) of ‘Spike’ protein of SARS-CoV (74% homologous to RBD of SARS-CoV-2). Leth Larsen et al also disclosed dose dependent and CRD mediated binding of SP-D with spike protein of SARS-CoV. Wu et al, 2009 teaches that serum levels of SP-D were elevated in patients with SARS related pneumonia and were correlated with anti-SARS-CoV IgG antibodies in SARS patients.

[008] Fungal pneumonia is an infectious process in the lungs caused by one or more endemic or opportunistic fungi. Endemic fungal pathogens (eg, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Paracoccidioides brasiliensis, Sporothrix schenckii, Cryptococcus neoformans ) and opportunistic fungal organisms (eg, Candida species, Aspergillus species, Mucor species) tend to cause pneumonia in patients with congenital or acquired defects in the host immune defenses. SP-D/rfhSP-D interacts with several respiratory fungal pathogens by recognizing several glycosylated ligands. Exogenous administration of rfhSP-D showed significant therapeutic potential in murine models of allergic and invasive mycoses (Madan et al, 2002; 2005; 2010).

[009] Surfactant deficiency is a common disorder in premature newborns and they frequently require manual ventilation for resuscitation during which lung injury occurs. Treatment with recombinant human SP-D (rhSP-D) containing surfactant inhibited lung inflammation and enhanced the resistance of surfactant to inhibition, supporting its potential usefulness for prevention of lung injury in the preterm newborn (Sato etal, 2010). The normal conversion of surfactant ultrastmcture requires SP-D that preferentially interacts with Pi-rich, newly secreted surfactant, causing lysis of surfactant lipid membranes, converting the lipid forms into smaller surfactant lamellated structures that are critical for surfactant uptake by type II cells and normal surfactant homeostasis (Ikegami el al., 2009). SP-D regulates the dramatic decreases in the surfactant pool size that occurs in the newborn period. Intratracheal recombinant human SP-D prevented shock caused by endotoxin released from the lung during ventilation in the premature newborn (Ikegami et al., 2006).

[0010] US8865643B2 discloses a recombinant fragment of surfactant protein D (rspd(nCRD)) polypeptide, fragment, homologue, variant or derivative thereof for use in a method of treatment or prophylaxis of a lung disease or a lung condition in which there is a need for a reduction in necrotic and apoptotic cells in the lung.

[0011] IN310696 discloses a formulation comprising essentially of a recombinant human SP- D (rhSP-D) protein of SEQ ID No. 2 consisting of 177 amino acid residues wherein 125 residues are positioned in the carbohydrate recognition domain, 28 residues in the neck region and 24 residues in the 8 N-terminal Gly-Xaa Yaa triplets or SEQ ID No. 3 consisting of 153 amino acid residues wherein 125 residues are positioned in the carbohydrate recognition domain, 28 residues in the neck region, active against HIV. However, it does not provide any teachings about a composition comprising essentially a recombinant fragment of human SP- D (rfhSP-D) protein and CaCk that is effective against SARS-CoV-2, as disclosed in the present application.

[0012] US2004/0043034A1 discloses a vaccine composition comprising at least one collectin and at least one immunogenic determinant. The collectin is selected from the group consisting of SP-A, SP-D, CL43, conglutinin, CL1 and mannose binding lectin (MBL).

[0013] US 2019/0388444 Al discloses a respirable, dry powder particle surfactant formulation for pulmonary delivery optionally comprising about 1% to about 10% by weight of the particle of a surfactant protein selected from the group consisting of SP-A, SP-B, SP-C and SP-D or any active fragment, derivative, or modification thereof.

[0014] None of the prior art documents discloses a composition comprising essentially a recombinant fragment of human SP-D (rfhSP-D) protein and CaCk directed against pulmonary infection including SARS-COV-2. The present composition comprising multifunctional rfhSP-D of SEQ ID NO. 2 is a potent viral entry inhibitor, immunomodulator, inducer of broad- spectrum anti-pathogen effects and lung-remodeling. [0015] The primary object of the present disclosure is to provide a composition comprising essentially a recombinant fragment of human SP-D (rfhSP-D) protein of SEQ ID NO. 2, CaCh and other ingredients directed against pulmonary infection including SARS-COV-2.

[0016] Another object of the present disclosure is to provide a nebulizer composition comprising essentially a recombinant fragment of human SP-D (rfhSP-D) protein of SEQ ID NO. 2 and CaCh directed against pulmonary infection including SARS-COV-2.

[0017] Yet another object of the present disclosure is to provide a dry powder composition comprising essentially a recombinant fragment of human SP-D (rfhSP-D) protein of SEQ ID NO. 2 and CaCh directed against pulmonary infection including SARS-COV-2.

[0018] Another object of the present disclosure is to provide a composition comprising essentially a recombinant fragment of human SP-D (rfhSP-D) protein of SEQ ID NO. 2 and CaCh useful as a monotherapy or adjunct therapy against SARS-COV-2.

SUMMARY OF INVENTION

[0019] In an aspect, the present disclosure relates to a pharmaceutical composition comprising a recombinant fragment of human surfactant protein D (rfhSP-D) of SEQ ID NO. 2 useful in treatment of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2). [0020] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, said composition comprising of 20- 50mg (2-75%) recombinant fragment of human surfactant protein D (rfhSP-D) of SEQ ID NO. 2; and 0.5- 1.4 mg (0.05-2.0%) CaCh.

[0021] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the recombinant fragment of human surfactant protein D (rfhSP-D) is glycosylated.

In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is a nebulizer composition and comprises: 2% (20 mg) rfhSP-D of SEQ ID NO. 2; 0.0567% CaCh (5mM) 0.550 mg; 0.827% NaCl (137 mM) 8.0145 mg; 0.0207% KC1 (2.7 mM) 0.201 mg; 0.1826% Na₂HP04 (10 mM) 1.77 mg; and 0.0318% KH2PO4 (1.8 mM) 0.309 mg per ml of water.

[0022] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is a dry powder composition and comprises 65.46 % (50 mg) rfhSP-D of SEQ ID NO. 2; 1.81 % (1.375 mg) CaCh; tri-leucine 32.73% (25mg).

[0023] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is a dry powder composition and comprises 70.05 % (50 mg) rfhSP-D of SEQ ID NO. 2; 1.92 % (1.375 mg) CaCh; L- Arginine 28.02% (20 mg).

[0024] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the pulmonary infection is caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2).

[0025] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is useful as a monotherapy or an adjunct therapy against pulmonary infection caused by SARS-CoV-2.

[0026] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the subject is a human.

[0027] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is preservative-free.

[0028] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the rfhSP-D of SEQ ID NO. 2 comprises of a signal peptide, N-terminal, a collagen domain, a neck domain, and a carbohydrate recognition domain; and wherein the rfhSP-D interacted with the spike protein of SARS-CoV-2, its receptor binding domain (RBD) as well as ACE- 2, their receptor in the human host.

BRIEF DESCRIPTION OF THE ACCOMPANYING DRAWINGS [0029] The following figures form part of the present specification and are included to further illustrate aspects of the present disclosure. The disclosure may be better understood by reference to the figures in combination with the detailed description of the specific embodiments presented herein.

[0030] Figure 1 depicts the tripartite interaction representation of S protein (Green) and rfhSP-D (Red) with ACE-2 (Blue) [A, B (zoomed view)] ACE-2 residues Serl9, Lys31, Glu35 and His34, interact with both S protein and rfhSP-D. The interactions between S protein and ACE-2 are deduced from the crystal structure (PDB ID: 6VW1) and between rfhSP-D, and ACE-2 protein are based on docked complexes. Individual intermolecular interactions between (C) S protein (Green) and ACE-2 (Blue); (D) S protein (Green) and rfhSP-D (Red) and (E) rfhSP-D (Red) and ACE-2 (Blue). The S protein residues Tyr449, Gln493 and Gln498, participate in intermolecular interactions with both ACE-2 and rfhSP-D.

[0031] Figure 2 depicts the docked poses of S protein and rfhSP-D complex with ACE2 (A-

C) and ACE2 and rfhSP-D complex with S protein (D).

[0032] Figure 3 depicts Recombinant Fragment of Human Surfactant Protein D (rfhSP-D) (nebulizer formulation) binding to the immobilised Spike protein (S protein) of the SARS- CoV-2 Virus and Immobilised rfhSP-D binds to hACE-2 in a dose-dependent but calcium- independent manner. The background was subtracted from all data points. The data were expressed as the mean of triplicates ± SD.

[0033] Figure 4 is a graphical representation illustrating that rfhSP-D (nebulizer formulation) inhibits the of interaction between Spike of SARS-CoV-2 and biotinylated hACE-2 in a calcium-independent manner.

[0034] Figure 5 is a graphical representation illustrating that rfhSP-D (nebulizer formulation) inhibits the interaction between Spike (RBD) of SARS-CoV-2 and biotinylated hACE-2 in a calcium-independent manner.

[0035] Figure 6 is a graphical representation illustrating the verification of reported TCID50 value of the clinical samples in Vero cells using MTT assay.

[0036] Figure 7 is a graphical representation illustrating the rfhSP-D (nebulizer formulation) pre-treatment of SARS-CoV-2 significantly inhibited its replication.

[0037] Figure 8 is a graphical representation illustrating the rfhSP-D (nebulizer formulation) pre-treatment of SARS-CoV-2 significantly inhibited its infectivity.

[0038] Figure 9 depicts the Recombinant Fragment of Human Surfactant Protein D (rfhSP-

D) (nebulizer formulation) binding to the immobilised Spike protein (S protein) of the SARS- CoV-2 Virus.

DETAILED DESCRIPTION OF THE INVENTION

[0039] Those skilled in the art will be aware that the present disclosure is subject to variations and modifications other than those specifically described. It is to be understood that the present disclosure includes all such variations and modifications. The disclosure also includes all such steps of the process, features of the product, referred to or indicated in this specification, individually or collectively, and any and all combinations of any or more of such steps or features.

Definitions [0040] For convenience, before further description of the present disclosure, certain terms employed in the specification, and examples are collected here. These definitions should be read in the light of the remainder of the disclosure and understood as by a person of skill in the art. The terms used herein have the meanings recognized and known to those of skill in the art, however, for convenience and completeness, particular terms and their meanings are set forth below.

[0041] The articles “a”, “an” and “the” are used to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article.

[0042] The terms “comprise” and “comprising” are used in the inclusive, open sense, meaning that additional elements may be included. It is not intended to be construed as “consists of only”.

[0043] Throughout this specification, unless the context requires otherwise the word “comprise”, and variations such as “comprises” and “comprising”, will be understood to imply the inclusion of a stated element or step or group of element or steps but not the exclusion of any other element or step or group of element or steps.

[0044] The term “including” is used to mean “including but not limited to”. “Including” and “including but not limited to” are used interchangeably.

[0045] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the disclosure, the preferred methods, and materials are now described. All publications mentioned herein are incorporated herein by reference. [0046] The present disclosure is not to be limited in scope by the specific embodiments described herein, which are intended for the purposes of exemplification only. Functionally equivalent products and methods are clearly within the scope of the disclosure, as described herein.

[0047] The present disclosure relates to a composition comprising recombinant fragment of human surfactant protein D (rfhSP-D) of SEQ ID NO. 2 useful in treatment of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2).

[0048] The present disclosure relates to a composition comprising essentially a recombinant fragment of human SP-D (rfhSP-D) protein of SEQ ID NO. 2, CaCk and other ingredients directed against pulmonary infection including SARS-CoV-2. [0049] In an aspect, the present disclosure relates to a pharmaceutical composition against pulmonary infection in a subject, said composition comprising of 2.0-75% recombinant fragment of human surfactant protein D (rfhSP-D) of SEQ ID NO. 2; and 0.05-2.0 % CaCh. [0050] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the recombinant fragment of human surfactant protein D (rfhSP-D) is glycosylated.

[0051] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is a nebulizer composition and comprises: 2.0% rfhSP-D of SEQ ID NO. 2; 0.0567 % CaCh; 0.827% NaCl (137 niM) 8.0145 mg; 0.0207% KC1 (2.7 mM) 0.201 mg; 0.1826% NazHPO^lO mM) 1.77 mg; and 0.0318% KFEPQ- il.S mM) 0.309 mg in water to make up the final volume to 1 ml. For the Nebuliser formulation, buffer solution was prepared using weighed amounts of CaCh, NaCl, KC1, Na2HP04, KH2PO4 were dissolved in 500ul of sterile water for injection (free of any preservatives and pyrogens). The solution pH was determined (should be within 7.3-7.5), was centrifuged for clarity, followed by sterile filtration using 0.22u filter in a biosafety hood. The manufacturer provided sterile aqueous stock solution of rfhSP-D produced in CHO cells (lOOmg/ml). The solution equivalent to 20 mg (200ul) was added to the buffer solution in the biosafety hood. The volume was made upto 1ml with sterile water for Injection and stored in sealed glass ampoules.

[0052] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is a dry powder composition and comprises 65-75 % rfhSP-D of SEQ ID NO. 2; 1.5-2.0 % CaCh; tri leucine 32.73% (25 mg) or L-Arginine 28.02% (20 mg). For the trileucine DPI formulation, buffer solution was prepared using weighed amounts of CaCh, and Trileucine in the biosafety hood. They were dissolved in 280ul of sterile water for injection (free of any preservatives and pyrogens) and absolute alcohol (120ul) (30 %v/v). The manufacturer provided sterile aqueous stock solution of rfhSP-D produced in CHO cells (lOOmg/ml). The solution equivalent to 50 mg (500ul) was added to the buffer solution in the biosafety hood. 180ul of absolute alcohol was added and solution was spray dried at 37°C. Spray dried powder was filled into hard gelatin capsules (size 4) in a clean room (100) and sealed in a bubble pack. For the L-Arginine DPI formulation, buffer solution was prepared using weighed amounts of CaCh, and L-Arginine in the biosafety hood. They were dissolved in 280ul of sterile water for injection (free of any preservatives and pyrogens) and absolute alcohol (120ul) (30 %v/v). The manufacturer provided sterile aqueous stock solution of rfhSP-D produced in CHO cells (lOOmg/ml). The solution equivalent to 50 mg (500ul) was added to the buffer solution in the biosafety hood. 180ul of absolute alcohol was added and solution was spray dried at 37°C. Spray dried powder was filled into hard gelatin capsules (size 4) in a clean room (100) and sealed in a bubble pack.

[0053] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is a dry powder composition and comprises 65.46 % (50 mg) rfhSP-D of SEQ ID NO. 2; 1.81 %

(1.375 mg) CaCh; tri-leucine 32.73% (25mg).

[0054] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is a dry powder composition and comprises 70.05 % (50 mg) rfhSP-D of SEQ ID NO. 2; 1.92 % (1.375 mg) CaCh; L-Arginine 28.02% (20 mg).

[0055] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the pulmonary infection is caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2).

[0056] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is useful as a monotherapy or an adjunct therapy against pulmonary infection caused by SARS-CoV-2.

[0057] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the subject is a human.

[0058] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the composition is preservative-free.

[0059] The primary structure of native, full length SP-D comprises of N-terminal domain, collagen triplet repeat domain, neck domain and CRD (375 aa, oligomerises to dodecamer, ~516kDa or fuzzy balls) and is of SEQ ID NO. 1 whereas the candidate molecule rfhSP-D (recombinant fragment of human SP-D; 177 aa, monomer 20kDa, homotrimer, ~60kDa) of SEQ ID NO. 2 comprising of a short stretch of eight Gly-X-Y triplets (179-202) (24 aa residues) with a substitution of serine for proline at position 2 followed by the 28 residue the a-helical coiled-coil neck region (residues 203-235) and the 125 aa globular CRD region (residues 236-355). [0060] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the rfhSP-D of SEQ ID NO. 2 comprises of a signal peptide, N-terminal, a collagen domain, a neck domain, and a carbohydrate recognition domain; and wherein the rfhSP-D interacted with the spike protein of SARS-CoV-2, its receptor binding domain (RBD) as well as ACE-2, their receptor in the human host.

[0061] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the recombinant fragment of human SP-D is produced in stably transfected mammalian CHO cells as well as in E.coli. [0062] The recombinant molecule prepared (rfhSP-D) showed significantly higher survival than full length native SP-D in an invasive mouse model of respiratory fungal pathogen (Madan et al, 2010). The enhanced biological efficacy is assigned to better and faster reachability of rfhSP-D to distal lungs with smaller size (~14 nm) than the full length dodecamer (~56nm) (Crouch et al., 1994). Importantly, rfhSP-D is relatively resistant to collagenases and proteases.

[0063] Approximately 40% of intranasally administered rfhSP-D can be detected in the cell- free lavage supernatant 1 hour after administration (Clark et al, 2002).

[0064] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the intranasal administration of a 10-pg dose of recombinant protein appeared to be sufficient to immediately replace endogenous pools. However, the administered protein is virtually undetectable in cell-free lavage 21 hours after administration, indicating that it is rapidly cleared from the alveolar space or becomes inaccessible to lavage.

[0065] SP-D/rfhSP-D interacts with a broad spectrum of Gram-negative and Gram-positive bacteria via the collectin CRD. The specific bacteria targeted by SP-D/rfhSP-D include Staphylococcus aureus, Klebsiella pneumonia, Mycobacterium tuberculosis and Escherichia coli. The consequence of SP-D/rfhSP-D binding varies depending on the bacteria, but can include agglutination, direct killing by permeabilization of the bacterial cell walls and enhancement of phagocytosis and increased respiratory burst by macrophages and neutrophils.

[0066] In an embodiment of the present disclosure, there is provided a pharmaceutical composition against pulmonary infection in a subject, wherein the rfhSP-D of SEQ ID NO. 2 acts as entry inhibitor and stops the SARS-CoV-2 march at the first step of the infection. [0067] Although the subject matter has been described in considerable detail with reference to certain preferred embodiments thereof, other embodiments are possible.

EXAMPLES

[0068] The disclosure will now be illustrated with working examples, which is intended to illustrate the working of disclosure and not intended to take restrictively to imply any limitations on the scope of the present disclosure. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice of the disclosed methods, the exemplary methods, devices and materials are described herein. It is to be understood that this disclosure is not limited to particular methods, and experimental conditions described, as such methods and conditions may vary.

Example 1

[0069] The clinical samples (throat and nasal swabs) (n=15) (Table 1) were from symptomatic contacts of lab-confirmed cases (Cat 2) (n=2), hospitalised severe acute respiratory infections (SARI) patients (Cat 4) (n=3), asymptomatic direct and high-risk contacts of lab-confirmed cases (Cat 5a) (n=7) and hospitalised symptomatic influenza-like illness (ILI) patients (Cat 6) (n=3) that had tested positive by RT-PCR test for SARS-CoV-2 at the Institute of Liver and Biliary Sciences, Delhi. Samples (n=15) that tested negative by RT-PCR test for SARS-CoV-2 were used as controls. The inclusion criteria for the cases were age (between 18-45 years) and a Ct value between 10 and 15 (18-45 years and an undetectable viral load for controls). The two groups showed no significant difference in their age and sex distribution. The 50% Tissue culture Infective Dose (TCID50) of the clinical samples was estimated using a template that utilized the Spearman & Karber method for calculation (14). The TCID50 value estimated was further confirmed via MTT assay. Briefly, 5 x 10⁴ Vero cells in Vero growth media [MEM Glutamax+10% FBS, 1% Penicillin- Streptomycin and 1% sodium pyruvate (Gibco)] were grown in a 96-well plate overnight. The clinical samples from the cases and controls at various dilutions were added to the cells, incubated for lh, wells were washed with PBS twice, and fresh Vero growth medium was added to the cells and incubated (96h, 37oC, 5% C02). MTT assay was performed to assess cell viability.

[0070] rfhSP-D from the Chinese Hamster Ovary (CHO) cells was produced by (transiently) transforming the CHO cells grown in the growth medium supplemented with 10% v/v fetal bovine serum (FBS), 2 mM 1-glutamine, 100 U/ml penicillin (Sigma-Aldrich), 100 pg/ml streptomycin (Sigma-Aldrich) and 1 mM sodium pyruvate (Sigma- Aldrich)] with plasmid pUK-Dl using lipofectamine. The cells were then grown in growth media supplemented with puromycin and left to grow at 37°C in the presence of 5% v/v C02 for approximately 3 days. These positively selected transformants were further passaged. rfhSP-D was expressed using glutamine synthetase expression system using GIBCO-tested cGMP-banked medium for the growth in suspension culture. CHO Medium used will be free from serum for suspension growth. The medium is also free from L-glutamine, proteins, hydrolysates, or miscellaneous components. After every round of 48 h culture, the supernatant was dialysed against affinity buffer (50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 5mM CaC12) overnight and then was loaded onto a maltose-agarose affinity column (15 ml). After washing the column extensively with the affinity buffer, rfhSP-D was eluted using lOmM EDTA buffer containing 50 mM Tris- HCl, pH 7.5 and 100 mMNaCl. Eluted rfhSP-D fractions were then tested for endotoxin levels using QCL-1000 Limulus amebocyte lysate system and TNF-alpha secretion by THP-1 cells. The purity of rfhSP-D was analysed by SDS-PAGE. Its immunoreactivity was determined via western blotting using a polyclonal antibody raised against full-length human SP-D purified from lung lavage.

[0071] Plasmid pUK-Dl containing cDNA for rfhSP-D (SEQ ID no. 1), under bacteriophage T7 promoter was used to produce rfhSP-D in Escherichia coli BL21(1DE3) pLysS. A primary inoculum of 10 ml bacterial culture, grown in LB containing 100 mg/ml ampicillin, 34 mg/ml chloramphenicol overnight in a shaking culture at 37 C, was inoculated into 500 ml LB and antibiotics and grown to A600 of 0.6-0.8. Cells were induced with 0.4 mM IPTG for 3 h and harvested by centrifugation. The cell pellet was re-suspended in the lysis buffer (50 mM Tris- HCl, 200 mM NaCl, 5 mM EDTA, 0.1% v/v Triton X-100, 0.1 mM PMSF, pH 7.5, 50 mg/ml lysozyme) and sonicated (5 cycles, 30 s each). The sonicate was harvested (12,000 g) and the rhSP-D recovered in the inclusion bodies was solubilized in 50 ml buffer I (50 mM Tris-HCl pH 7.5, 100 mM NaCl) containing 10 mM 2-mercaptoethanol and 8 M Urea. The resolubilized material was then dialyzed stepwise against buffer I contain 4 M urea, 2 M urea, 1 M urea and no urea, each for 2 h. The dialysate, clarified by centrifugation (12,000g, 10 min), was then loaded onto a Q-Sepharose anion exchange resin (Pharmacia), washed extensively with buffer I and eluted with 400 mM NaCl. The peak fractions were loaded onto maltose-agarose column in buffer I- 10 mM CaC12, washed extensively, and the bound rhSP-D was eluted with buffer I- 10 mM EDTA. The contaminating level of endotoxin present in the rhSP-D preparation was minimized by passing the rhSP-D through Polymyxin B column (Detoxi-Gel, Pierce, UK). [0072] The rfhSP-D from the Chinese Hamster Ovary (CHO) cells was characterized and compared with rfhSP-D derived from Escherichia coli BL21(1DE3) pLysS. Table 1 below provides the characterization details of rfhSP-D derived from CHO cells and E-coli.

Table 1: Characterization of purified rfhSP-D-E. coli and rfhSP-D-CHO

Example 2

Binding analysis of rfhSP-D with SARS-COV-2 protein, spike (S) and hACE-2 using in silica docking, [0073] The rfhSP-D trimer (PDB ID: 1PW9) was blind docked with a) RBD of S protein in open conformation (PDB ID: 6VYB) and b) dimeric ACE2 (PDB ID: 6VW1). Top 100 docked poses of the docking experiments were selected and further refined using Fire Dock web server (16) for calculation of global free energy. The top five refined structures were filtered based on interactions between RBM of S protein, C-Type Lectin Domain (CTLD: aa 240-355) of rfhSP-D and N-terminal of ACE2.

[0074] The effect of binding of trimeric rfhSP-D to S-protein and dimeric ACE2 on ACE2-S protein interaction was evaluated by further docking the docked complex of a) S protein and rfhSP-D with ACE2 and b) ACE2 and rfhSP-D with S protein. Patch dock web server (15) was used for all docking experiments.

[0075] The redocked complex of ACE2 and S protein had root mean square deviation (RMSD) of 7.9 A. The close agreement between the docked and crystal structures validated the docking protocol used in the study. In case of docked solutions for S protein and rfhSP- D; the third ranked docked pose with binding energy of -20.63 kcal/mol exhibited rfhSP-D interactions with RBM residues Tyr449, Gln493 Gln498 implying that rfhSP-D could bind to Spike S in a manner that can inhibit ACE2 - S protein interaction, as shown in Figure 1 and Table 1 below. To ascertain this hypothesis, the docked complex of S protein with rfhSP-D was docked to ACE2. S protein and rfhSP-D bound to ACE2 via common interacting residues. [0076] The top ranked docked structure of ACE2 and rfhSP-D had binding energy of -24.30 kcal/mol. In this pose, rfhSP-D interacted with the virus-binding hotspot residues Serl9, Lys31, His34 and Glu35 of ACE2, implying that rfhSP-D could bind to ACE2 in a manner that can inhibit ACE2-S protein interaction (Table 1, Figure 1). To corroborate this postulation, the docked complex of ACE2 with rfhSP-D was docked to Spike S. Top ranked pose of ACE2-rfhSP-D complex docked with open S protein had binding energy of -33.01 kcal/mol and several common interactions between rfhSP-D and ACE2 with S protein, as shown in Figure 2. The docking experiments lead us to infer that rfhSP-D could bind to both ACE2 and Spike S and prevent ACE2-S protein interaction.

Table 1: Results of docking of S protein, ACE-2, and rfhSP-D

The S protein residues in bold are predicted to be part of the common binding site for ACE2 and rfhSP-D. ^$The ACE2 residues in bold interact with both S protein and rfhSP-D (docked structure).

^@The structural coordinates of Phe486 is missing in the open conformation S protein (PDB ID: 6VYB). Example 3

ELISA test to determine the binding of present rfhSP-D with the ‘S’ protein or its RBD of SARS-CoV-2

[0077] Assays to determine the binding of the rfhSP-D with the S protein or its RBD of SARS-CoV-2 were performed using the SARS-CoV-2 (COVID-19) Inhibitor Screening Kit from Acrobiosystems (EP-105). rfhSP-D-S protein interaction was determined by coating the wells with 0.3 pg/ml S protein and incubated with present rfhSP-D nebulizer formulation (20, 10 and 5 pg/ml) for 1 hour at 37°C. The wells were then incubated with polyclonal or monoclonal antibodies against SP-D (1 mg/ml) and probed with their respective secondary antibodies conjugated with HRP. The binding was detected using 3, 3', 5,5'- Tetramethylbenzidine (TMB) substrate and absorbance was recorded at 450 nm. The binding of Full-length Surfactant Protein D (FL SP-D) (20 pg/ml) to S protein was also assessed in a similar manner. A parallel experiment was carried out using present rfhSP-D nebulizer formulation (20, 10 and 5 pg/ml) supplemented with lOmM EDTA and probed with polyclonal antibodies against SP-D to evaluate if the S protein-rfhSP-D binding was calcium- dependent.

[0078] rfhSP-D/FL SP-D to ACE-2 binding was evaluated by coating present rfhSP-D nebulizer formulation/FL SP-D (0.1 pg/ml) and probed with biotinylated hACE-2 (0.12, 0.06 and O.OOpg/ml). The binding was detected using streptavidin tagged with HRP and the colour was developed.

[0079] In a separate experiment to assess if rfhSP-D inhibited the interaction between the S protein or its RBD with biotinylated human hACE-2, present rfhSP-D nebulizer formulation (5, 1 and 0 pg/ml) was preincubated with the coated S protein or its RBD followed by addition of biotinylated ACE-2. The S protein-hACE-2 binding was measured by probing the wells with the HRP tagged Streptavidin antibody and inhibition was measured as per EP-105 manufacturer’s instructions. Present rfhSP-D nebulizer formulation (5 pg/ml) supplemented with lOmM EDTA was used in a similar manner to evaluate if the inhibition occurred in a calcium-dependent manner.

[0080] rfhSP-D binds to the immobilised S protein of the SARS-CoV-2 and hACE2: The possible binding between rfhSP-D and the S protein hinted by the docking analysis was confirmed in vitro by performing an indirect ELISA. rfhSP-D was found to bind the immobilised S protein in a dose-dependent manner as shown in Figure 3(a). No significant difference was observed between the binding of S protein to either rfhSP-D derived from E. coli or the rfhSP-D derived from CHO cells. However, a significant difference in the reported absorbance was observed based on the primary antibody used. S protein-rfhSP-D binding that was probed with the polyclonal antibody against SP-D reported a significantly higher absorbance when compared to the wells that were probed with a monoclonal antibody directed against the CRD of SP-D. This difference suggests involvement of CRD of rfhSP-D with the spike protein and therefore not available for interaction with the monoclonal antibody. S protein was also found to bind to the FLSP-D used. The treatment of rfhSP-D with lOmM EDTA did not significantly affect the binding efficiency of rfhSP-D to S protein, as shown in Figure 3(b), indicating that the presence/absence of Ca²⁺ does not seem to affect the binding. Hence, we can conclude that rfhSP-D binds to the S protein in a dose-dependent but a calcium- independent manner. In a similar parallel experiment, the binding of rfhSP-D to ACE2 was assessed, and it was found to occur in a dose-dependent manner in all tested concentrations, irrespective of the source of the SP-D used, as shown in Figure 3(c) of the present disclosure. [0081] rfhSP-D inhibits the interaction of S protein and its RBD with biotinylated hACE-2 in a calcium-independent manner: Since rfhSP-D was found to bind to the S protein and ACE- 2, and as both rfhSP-D and ACE-2 were predicted to share the same binding site on S protein, rfhSP-D mediated inhibition of the interaction between the RBD of S protein of SARS-CoV- 2 and ACE-2 was assessed using a simple colorimetric ELISA platform.

[0082] The experiment was set up by coating the wells with either the S protein or its RBD domain and that was preincubated with present rfhSP-D nebulizer formulation followed by determining their binding to biotinylated hACE-2. The functionality and the range of the assay were initially assessed by verifying if the assay could detect the binding of hACE-2 at a concentration of 0.12 pg/ml and 0.06 pg/ml. The binding was observed to occur in a dose- dependent manner at all tested concentrations, confirming that the assay works and can detect binding between S protein and its RBD domain with hACE-2 at a concentration as low as 60ng/ml. A decrease in binding between S protein and hACE-2 was observed as the concentration of rfhSP-D increased, as shown in Figure 4 and Figure 5 of the present disclosure. Approximately, a 50% decrease in S protein-hACE-2 binding was observed as rfhSP-D concentration increased 5-fold, as shown in Figure 4(a) and 4(b). A similar result was observed between the binding of the RBD of S protein and hACE-2. An 8-fold increase in the concentration of rfhSP-D was found to decrease SRBD: hACE-2 binding by -25%, as shown in Figure 5(a) and 5(b). As before, the source of rfhSP-D (E. ColU CHO cells) did not significantly affect the interaction between S protein or its RBD domain with hACE-2. No significant difference was observed between the samples with lOmM EDTA and without EDTA in terms of rfhSP-D mediated S protein/SRBD-hACE-2 binding, as shown in Figure 4(c) and Figure 5(c). Hence, rfhSP-D mediated inhibition of the interaction between the RBD of S protein or the S protein itself with biotinylated hACE-2 occurred in a calcium-independent manner.

Example 4

Vero Cell Replication Assay to study the effect of rfhSP-D on SARS-CoV-2 viral infection.

[0083] Vero cell line (ATCC® CCL-81™) (5x10⁴) were cultured in serum- free MEM. SARS-CoV-2 positive clinical samples (100 TCID50/ well, MOI 0.01) were preincubated with present rfhSP-D nebulizer formulation [0 pg/ml (0 pM), 50 pg/ml (~2.5pM) or 100 pg/ml (~5pM)] in MEM containing 5mM CaC12 for lhour at room temperature and lhour at 4oC (Al-Ahdal et al., 2018). SARS-CoV-2 negative clinical samples (volume equivalent to 100 TCID50 of the age and sex matched SARS-CoV-2 positive sample/ well, MOI 0.01) were preincubated with rfhSP-D in MEM containing 5mM CaCk for lhour at room temperature and lhour at 4°C. This pre-treated or untreated virus was added to the cells and was incubated for lhour incubation at 37°C, 5% CO2. Following PBS washes, infection medium (MEM+0.3% BSA) was added to the cells and incubated for 24 hours to assess replication. The harvested cells were subjected to total RNA extraction using the Perkin Elmer automated extractor. Real-time RT-PCR for SARS-CoV-2 was carried out using Pathodetect kits from MyLabs, as per manufacture’ s protocol. For the replication analysis of SARS-CoV-2, Ct value for SARS-CoV-2 RNA dependent RNA polymerase (RdRp) gene was used for analysis. Cells incubated with rfhSP-D, without virus was used protein control.

[0084] The effect of rfhSP-D on viral infection was assessed by culturing Vero cells (5xl0⁵) in serum-free MEM. SARS-CoV-2 positive clinical samples (500 TCID50/ well, MOI 0.05) were treated with present rfhSP-D nebulizer formulation. SARS-CoV-2 negative clinical samples (volume equivalent to 500 TCID™ of the SARS-CoV-2 positive sample/ well, MOI 0.05) were also treated with rfhSP-D. After the addition of the infection medium, the cells were incubated only for 2hours, after which they were harvested, and Real-time RT-PCR was performed using the same controls and parameters described above.

[0085] rfhSP-D treatment inhibits SARS-CoV-2 infection and replication: As rfhSP-D has been known to induce apoptosis in cancer and immortalised cells (29-32), the effect of present rfhSP-D nebulizer formulation on Vero cells was assessed using MTT assay. rfhSP-D showed no significant effect on the cell viability of Vero cells post-treatment. At the outset, the TCID50 values of the clinical samples were obtained by evaluating the cytopathicity using MTT assay. As expected, when Vero cells were challenged with 100 TCID50, or 50 TCID50 of viral samples from SARS-CoV-2 cases, a 50% or 25% reduction in cell viability was observed respectively, compared to the viability of uninfected Vero cells, confirming the assayed TCID50 values, as shown in Figure 6. Samples from the control samples showed no significant difference in the cell viability than the uninfected Vero cells when the control sample volumes equivalent to 100 TCID50 and 50 TCID50 of the cases were used.

[0086] The effect of present rfhSP-D formulations on the replication of SARS-CoV-2 (100TCID5o/well; MOI 0.01) in Vero cells was measured by studying the expression levels on the RdRp gene by RT-PCR 24 hours post-infection. Pre-treatment of the positive samples (n=15) comprising of SARS-CoV-2 with rfhSP-D lead to a reduction of RdRp gene expression in a dose-dependent manner, as shown in Figure 7. The pre-treatment of samples from all categories of SARS-CoV-2 positive cases [as representatives, the figure 7 shows the data for 49251 (Cat 2) and 49277 (Cat4)] with 2.5mM present rfhSP-D nebulizer formulation led to ~4.5-fold reduction (-4.5 log2) of RdRp transcript compared to the rfhSP-D untreated positive sample challenged Vero cells. The trileucine DPI formulation (A) and L-arginine DPI formulation (B) (resuspended in the medium equivalent to 2.5mM of rfhSP-D) showed significantly higher 4.82 and 5.14-fold reduction of RdRp transcript, respectively. There was no significant difference in the Ct values of RdRp gene from the untreated and control sample treated Vero cells. Similarly, pre-treatment with 5 mM rfhSP-D resulted in ~5.5-fold reduction (-5.5 log2) of RdRp mRNA expression. The trileucine DPI formulation (A) and L-arginine DPI formulation (B) (resuspended in the medium equivalent to 5mM of rfhSP-D) showed significantly higher 5.76 and 6.23-fold reduction of RdRp transcript respectively. Remdesivir, one of the treatments that was proposed for COVID-19, which functions by inhibiting viral RNA synthesis, was found to inhibit SARS-CoV-2 replication by ~4-fold (-4 log2). Hence, rfhSP-D blocked SARS-CoV-2 infection and inhibited the replication of SARS-CoV-2 significantly better than Remdesivir at both tested concentrations (2.5 mM and 5 mM rfhSP- D).

[0087] As rfhSP-D was found to interact with S protein and ACE-2, proteins that play an integral role in viral host cell recognition and entry, the role of rfhSP-D in viral infectivity was assessed in a similar manner to replication. Vero cells infected with SARS-CoV-2 positive samples (500TCID5o/well, MOI 0.05) showed a rfhSP-D (nebulizer formulation) dose-dependent decrease in the expression levels of the RdRp gene, 2h post-infection, as shown in Figure 8. Clinical samples from all the categories of SARS-CoV-2 patients [As representatives, figure 8 shows the data from 48172 (Cat 4) and 48301 (Cat 5a)] showed ~ 1.25-fold reduction (-1.25 log 10) or ~ 2-fold reduction (-2 log 10) in RdRp gene expression with the samples pretreated with either 2.5mM or 5 mM respectively of rfhSP-D (nebulizer formulation). Remdesivir was used as a negative control (Remdesivir does not inhibit SARS- CoV-2 infection), and no significant effect was observed. Thus, this experiment confirmed that pretreatment of SARS-CoV-2 in the clinical sample with rfhSP-D made S protein unavailable to interact with the ACE-2 receptor on the host cell, thus, reducing the infectivity of the virus and subsequent viral replication in a dose-dependent manner.

Claims

Claims:

1. A pharmaceutical composition comprising a recombinant fragment of human surfactant protein D (rfhSP-D) of SEQ ID NO. 2 useful in treatment of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2).

2. A pharmaceutical composition against pulmonary infection in a subject, said composition comprising of 20-50mg (2-75%) recombinant fragment of human surfactant protein D (rfhSP-D) of SEQ ID NO. 2; and 0.5- 1.4 mg (0.05-2.0 %) CaCh.

3. The composition as claimed in claim 2, wherein the recombinant fragment of human surfactant protein D (rfhSP-D) is glycosylated.

4. The composition as claimed in claim 2, wherein the composition is a nebulizer composition and comprises: 2% (20 mg) rfhSP-D of SEQ ID NO. 2; 0.0567% CaCh (5mM) 0.550 mg; 0.827% NaCl (137 mM) 8.0145 mg; 0.0207% KC1 (2.7 mM) 0.201 mg; 0.1826% NaaHPOrQO mM) 1.77 mg; and 0.0318% KlEPOif l.S mM) 0.309 mg per ml of water.

5. The composition as claimed in claim 2, wherein the composition is a dry powder composition and comprises 65.46 % (50 mg) rfhSP-D of SEQ ID NO. 2; 1.81 % (1.375 mg) CaCh; tri-leucine 32.73% (25mg).

6. The composition as claimed in claim 2, wherein the composition is a dry powder composition and comprises 70.05 % (50 mg) rfhSP-D of SEQ ID NO. 2; 1.92 % (1.375 mg) CaCh; L- Arginine 28.02% (20 mg).

7. The composition as claimed in claim 2, wherein the pulmonary infection is caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2).

8. The composition as claimed in claims 2-7, wherein the composition is useful as a monotherapy or an adjunct therapy against pulmonary infection caused by SARS- CoV-2.

9. The composition as claimed in claim 2, wherein the subject is a human.

10. The composition as claimed in claim 2-9, wherein the composition is preservative- free.

11. The composition as claimed in claim 2-10, wherein the rfhSP-D of SEQ ID NO. 2 comprises of a signal peptide, N-terminal, a collagen domain, a neck domain, and a carbohydrate recognition domain; and wherein the rfhSP-D interacted with the spike protein of SARS-CoV-2, its receptor binding domain (RBD) as well as ACE-2, their receptor in the human host.