Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yes ☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13 (a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒.

As of November 5, 2021, there were 439,590,272 shares of registrant’s common stock outstanding.

TONIX PHARMACEUTICALS HOLDING CORP.
CONDENSED CONSOLIDATED BALANCE SHEETS
(In Thousands, Except Par Value and Share Amounts)

TONIX PHARMACEUTICALS HOLDING CORP.
CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
(In Thousands, Except Share and Per Share Amounts)

TONIX PHARMACEUTICALS HOLDING CORP.
CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS
(In Thousands)

TONIX PHARMACEUTICALS HOLDING CORP.

CONDENSED CONSOLIDATED STATEMENT OF STOCKHOLDERS’ EQUITY

NINE MONTHS ENDED SEPTEMBER 30, 2020

(In Thousands, Except Share and Per Share Amounts)

(unaudited)

													Accumulated
	Series B Convertible									Additional			Other
	Preferred stock					Common stock				Paid in			Comprehensive			Accumulated
	Shares			Amount		Shares		Amount		Capital			Gain (loss)			Deficit			Total
Balance, December 31, 2019		—		$	—		8,531,504	$	9	$	226,524		$	(46	)	$	(217,070	)	$	9,417
Issuance of common stock in exchange for exercise of warrants in February and March 2020 ($0.57 per share)		—			—		13,111,999		13		7,461			—			—			7,474
Deemed dividend in connection with repricing of November 2019 warrants		—			—		—		—		451			—			—			451
Warrant deemed dividend		—			—		—		—		(451	)		—			—			(451	)
Issuance of Series B Convertible preferred stock and common stock warrants in February 2020 ($1,000.00 per share, net of transactional expenses of $711)		5,313			—		—		—		4,602			—			—			4,602
Beneficial conversion feature in connection with issuance of Series B Convertible preferred stock		—			—		—		—		1,260			—			—			1,260
Preferred stock deemed dividend		—			—		—		—		(1,260	)		—			—			(1,260	)
Issuance of common stock and common stock warrants in February 2020 ($0.57 per share, net of transactional expenses $292)		—			—		3,837,000		4		1,891			—			—			1,895
Issuance of common stock upon conversion of Series B Convertible preferred stock		(5,313	)		—		9,321,053		9		(9	)		—			—			—
Issuance of common stock in March 2020 ($1.10 per share, net of transactional expenses of $1,221)		—			—		14,550,000		14		14,770			—			—			14,784
Employee stock purchase plan		—			—		1,578		—		2			—			—			2
Stock-based compensation		—			—		—		—		360			—			—			360
Foreign currency transaction gain		—			—		—		—		—			(14	)		—			(14	)
Net loss		—			—		—		—		—			—			(7,273	)		(7,273	)
Balance, March 31, 2020		—			—		49,353,134		49		255,601			(60	)		(224,343	)		31,247
Issuance of common stock in June 2020 under the equity line		—			—		464,471		1		277			—			—			278
Issuance of common stock in May and June 2020 under At-the-market offering, net of transaction expenses of $1,131		—			—		52,986,301		53		34,089			—			—			34,142
Issuance of common stock in the acquisition of Trigemina assets		—			—		2,000,000		2		1,358			—			—			1,360
Stock-based compensation		—			—		—		—		733			—			—			733
Foreign currency transaction gain		—			—		—		—		—			(9	)		—			(9	)
Net loss		—			—		—		—		—			—			(14,179	)		(14,179	)
Balance, June 30, 2020		—			—		104,803,906		105		292,058			(69	)		(238,522	)		53,572
Issuance of common stock in July 2020, net of transaction expenses of $829		—			—		20,940,000		21		9,620			—			—			9,641
Issuance of common stock in September 2020 under At-the-market offering, net of transactional expenses of $267		—			—		9,282,236		9		7,997			—			—			8,006
Issuance of common stock in exchange for exercise of warrants in July and August 2020 (see Note 9)		—			—		4,533,404		5		2,417			—			—			2,422
Issuance of commitment shares under 2020 Purchase Agreement		—			—		600,000		—		—			—			—			—
Stock-based compensation		—			—		—		—		912			—			—			912
Foreign currency transaction loss		—			—		—		—		—			5			—			5
Net loss		—			—		—		—		—			—			(11,990	)		(11,990	)
Balance, September 30, 2020		—		$	—		140,159,546	$	140	$	313,004		$	(64	)	$	(250,512	)	$	62,568

Nevada		26-1434750
(State or other jurisdiction of incorporation or organization)		(I.R.S. Employer Identification No.)

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock	TNXP	The NASDAQ Global Market

PART I.	FINANCIAL INFORMATION

	ITEM 1.	Financial Statements

		Condensed consolidated balance sheets as of September 30, 2021 (unaudited) and December 31, 2020	3

		Condensed consolidated statements of operations for the three and nine months ended September 30, 2021 and 2020 (unaudited)	4

		Condensed consolidated statements of comprehensive loss for the three and nine months ended September 30, 2021 and 2020 (unaudited)	5

		Condensed consolidated statements of stockholders’ equity for the three and nine months ended September 30, 2021 and 2020 (unaudited)	6-7

		Condensed consolidated statements of cash flows for the nine months ended September 30, 2021 and 2020 (unaudited)	8

		Notes to condensed consolidated financial statements (unaudited)	9-23

	ITEM 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	24-36

	ITEM 3.	Quantitative and Qualitative Disclosures about Market Risk	37

	ITEM 4.	Controls and Procedures	37

PART II.	OTHER INFORMATION

	ITEM 1.	Legal Proceedings	37
	ITEM 1A.	Risk Factors	37
	ITEM 2.	Unregistered Sales of Equity Securities and Use of Proceeds	38
	ITEM 3.	Defaults Upon Senior Securities	38
	ITEM 4.	Mine Safety Disclosures	38
	ITEM 5.	Other Information	38
	ITEM 6.	Exhibits	38

	SIGNATURES		39

	September 30, 2021			December 31, 2020
	(unaudited)
ASSETS
Current assets:
Cash and cash equivalents	$	182,970		$	77,068
Prepaid expenses and other		12,112			10,921
Total current assets		195,082			87,989

Property and equipment, net		18,233			8,571

Right-of-use assets, net		1,068			1,258
Security deposit		31			5
Restricted cash		240			240
Intangible asset		120			120

Total assets	$	214,774		$	98,183

LIABILITIES AND STOCKHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	7,964		$	4,598
Accrued expenses and other current liabilities		3,479			4,626
Lease liability, current		583			595
Total current liabilities		12,026			9,819

Lease liability, net of current portion		530			716

Total liabilities		12,556			10,535

Commitments (See Note 16)

Stockholders’ equity:

Preferred stock, $0.001 par value; 5,000,000 shares authorized
Series B Convertible Preferred stock, $0.001 par value, 5,313 shares designated as of September 30, 2021 and December 31, 2020, 0 issued and outstanding		—			—
Series A Convertible Preferred stock, $0.001 par value, 7,938 shares designated as of September 30, 2021 and December 31, 2020, 0 issued and outstanding		—			—
Common stock, $0.001 par value; 800,000,000 and 400,000,000 shares authorized as of September 30, 2021 and December 31, 2020, respectively; 403,673,156 and 206,008,683 shares issued and outstanding as of September 30, 2021 and December 31, 2020, respectively		404			206
Additional paid in capital		532,162			355,037
Accumulated deficit		(330,267	)		(267,533	)
Accumulated other comprehensive loss		(81	)		(62	)

Total stockholders’ equity		202,218			87,648

Total liabilities and stockholders’ equity	$	214,774		$	98,183


	Three Months Ended September 30,						Nine Months Ended September 30,
	2021			2020			2021			2020
COSTS AND EXPENSES:
Research and development	$	13,082		$	8,813		$	46,542		$	24,060
General and administrative		5,453			3,186			16,291			9,428
		18,535			11,999			62,833			33,488

Operating loss		(18,535	)		(11,999	)		(62,833	)		(33,488	)

Interest income, net		7			9			99			46

Net loss		(18,528	)		(11,990	)		(62,734	)		(33,442	)

Warrant deemed dividend		—			—			—			(451	)
Preferred stock deemed dividend		—			—			—			(1,260	)

Net loss available to common stockholders	$	(18,528	)	$	(11,990	)	$	(62,734	)	$	(35,153	)

Net loss per common share, basic and diluted	$	(0.05	)	$	(0.09	)	$	(0.19	)	$	(0.49	)

Weighted average common shares outstanding, basic and diluted		366,425,157			127,199,834			329,550,525			71,329,221

Large accelerated filer	☐	Accelerated filer	☐
Non-accelerated filer	☒	Smaller reporting company	☒
		Emerging growth company	☐


	Nine Months Ended September 30,
	2021			2020
CASH FLOWS FROM OPERATING ACTIVITIES:
Net loss	$	(62,734	)	$	(33,442	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization		23			20
Common stock issued to acquire in-process research and development		3,000			1,360
Stock-based compensation		5,603			2,005
Changes in operating assets and liabilities:
Prepaid expenses and other		(1,217	)		(3,662	)
Accounts payable		3,370			(1,301	)
Operating lease liabilities and ROU asset, net		(10	)		8
Accrued expenses and other current liabilities		(1,147	)		360
Net cash used in operating activities		(53,112	)		(34,652	)

CASH FLOWS FROM INVESTING ACTIVITIES:
Purchase of property and equipment		(9,685	)		(4,030	)
Net cash used in investing activities		(9,685	)		(4,030	)

CASH FLOWS FROM FINANCING ACTIVITIES:
Proceeds from exercise of warrants		2			9,896
Proceeds from ESPP		96			2
Proceeds, net of $0 and $711 expenses, from sale of preferred stock		—			4,602
Proceeds, net of $9,329 and $3,740 expenses, from sale of common stock and warrants		168,622			68,746
Net cash provided by financing activities		168,720			83,246

Effect of currency rate change on cash		(21	)		(16	)

Net increase in cash, cash equivalents and restricted cash		105,902			44,548
Cash, cash equivalents and restricted cash beginning of the period		77,308			11,349

Cash, cash equivalents and restricted cash end of period	$	183,210		$	55,897

Supplemental disclosures of cash flow information:
Warrants deemed dividend	$	—		$	451
Series B Convertible preferred stock and deemed dividend	$	—		$	1,260


		September 30, 2021		December 31, 2020
		(in thousands)
Cash and cash equivalents	$	182,970	$	77,068
Restricted cash		240		240
Total	$	183,210	$	77,308

	2021	2020
Warrants to purchase common stock	644,906	650,806
Options to purchase common stock	25,780,349	10,209,286
Totals	26,425,255	10,860,092

		September 30 2021			December 31 2020
		(in thousands)
Property and equipment, net:
Land and Buildings	$	5,713		$	5,713
Construction in progress		12,374			2,800
Office furniture and equipment		496			385
Leasehold improvements		23			23
		18,606			8,921
Less: Accumulated depreciation and amortization		(373	)		(350	)
	$	18,233		$	8,571